From 429e1c3a43f71cdeed8e70044db74d3289841316 Mon Sep 17 00:00:00 2001 From: AliciaMstt Date: Tue, 9 Apr 2024 22:18:43 -0600 Subject: [PATCH] change aliciamstt to ccgenetics in all links --- README.md | 2 +- .../DNA-based-monitoring-indicator.md | 4 ++-- .../Gen_div_advantages.md | 4 ++-- .../Genetic_div_indicators.md | 6 ++--- docs/2_Theoretical_background/Ne-500.md | 10 ++++----- docs/2_Theoretical_background/PM-indicator.md | 8 +++---- .../What-is-a-population.md | 6 ++--- .../Extinct_extant_populations.md | 4 ++-- .../Howto_define_populations.md | 4 ++-- docs/3_Howto_guides_examples/Ne_Nc-ratio.md | 4 ++-- .../Populations_sizes.md | 8 +++---- .../Reference_period.md | 4 ++-- docs/3_Howto_guides_examples/uncertainty.md | 4 ++-- docs/3_Quickstart/Quickstart.md | 22 +++++++++---------- docs/4_Species_list/Species_list.md | 4 ++-- .../Example_assessments.md | 4 ++-- docs/5_Data_collection/Data_sources.md | 8 +++---- docs/5_Data_collection/Kobo_toolbox_help.md | 6 ++--- docs/5_Data_collection/Recommended_data.md | 14 ++++++------ docs/5_Data_collection/Web_tool.md | 6 ++--- .../Country_ind_values.md | 4 ++-- .../6_Calculations_and_reporting/Equations.md | 6 ++--- .../6_Calculations_and_reporting/R_scripts.md | 12 +++++----- .../Temporal_change.md | 4 ++-- docs/7_Glossary/Glossary.md | 8 +++---- docs/Contact_cite/Contact_cite.md | 2 +- .../References_and-resources.md | 4 ++-- index.md | 14 ++++++------ 28 files changed, 93 insertions(+), 93 deletions(-) diff --git a/README.md b/README.md index e62ed98..63c397f 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ This repository host the guideline materials and documentation for the assessment of species genetic diversity using genetic diversity indicators. -You can browse the documentation at https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/ +You can browse the documentation at https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/ ## Licensing and Attribution diff --git a/docs/2_Theoretical_background/DNA-based-monitoring-indicator.md b/docs/2_Theoretical_background/DNA-based-monitoring-indicator.md index d03bbc4..b8543fd 100644 --- a/docs/2_Theoretical_background/DNA-based-monitoring-indicator.md +++ b/docs/2_Theoretical_background/DNA-based-monitoring-indicator.md @@ -24,5 +24,5 @@ The DNA-based monitoring indicator is measured at the species level, e.g. each s -[Previous: PM indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html#populations-maintained-indicator){: .btn .btn-blue .mr-4 } -[Next: Genetic diversity - advantages](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Gen_div_advantages.html#genetic-diversity---advantages){: .btn .btn-green } +[Previous: PM indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html#populations-maintained-indicator){: .btn .btn-blue .mr-4 } +[Next: Genetic diversity - advantages](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Gen_div_advantages.html#genetic-diversity---advantages){: .btn .btn-green } diff --git a/docs/2_Theoretical_background/Gen_div_advantages.md b/docs/2_Theoretical_background/Gen_div_advantages.md index 459f450..517af84 100644 --- a/docs/2_Theoretical_background/Gen_div_advantages.md +++ b/docs/2_Theoretical_background/Gen_div_advantages.md @@ -35,5 +35,5 @@ Genetic diversity indicators have multiple practical uses beyond reporting. They -[Previous: DNA-based monitoring indicators](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html#dna-based-genetic-monitoring-indicator){: .btn .btn-blue .mr-4 } -[Next: What is a population?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer){: .btn .btn-green } +[Previous: DNA-based monitoring indicators](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html#dna-based-genetic-monitoring-indicator){: .btn .btn-blue .mr-4 } +[Next: What is a population?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer){: .btn .btn-green } diff --git a/docs/2_Theoretical_background/Genetic_div_indicators.md b/docs/2_Theoretical_background/Genetic_div_indicators.md index 87508e2..cd4a17c 100644 --- a/docs/2_Theoretical_background/Genetic_div_indicators.md +++ b/docs/2_Theoretical_background/Genetic_div_indicators.md @@ -21,7 +21,7 @@ It is therefore imperative that all populations be maintained, and that populati . -Although there are no global, standardized databases for reporting the number of species’ population and their census sizes, this information is available for many species in various other sources (e.g., reports, national databases, scientific literature, government gazettes, consulting experts and knowledge holders, community science, etc.). This guidance document will help you gather and use the necessary data, from diverse sources, in a standardized way (see [Data Collection](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection)). +Although there are no global, standardized databases for reporting the number of species’ population and their census sizes, this information is available for many species in various other sources (e.g., reports, national databases, scientific literature, government gazettes, consulting experts and knowledge holders, community science, etc.). This guidance document will help you gather and use the necessary data, from diverse sources, in a standardized way (see [Data Collection](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection)). -[Previous: Overview](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/#guideline-materials-and-documentation-for-the-genetic-diversity-indicators){: .btn .btn-blue .mr-4 } -[Next: Ne 500 indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator){: .btn .btn-green } +[Previous: Overview](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/#guideline-materials-and-documentation-for-the-genetic-diversity-indicators){: .btn .btn-blue .mr-4 } +[Next: Ne 500 indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator){: .btn .btn-green } diff --git a/docs/2_Theoretical_background/Ne-500.md b/docs/2_Theoretical_background/Ne-500.md index 08c70b7..9a75736 100644 --- a/docs/2_Theoretical_background/Ne-500.md +++ b/docs/2_Theoretical_background/Ne-500.md @@ -11,7 +11,7 @@ nav_order: 2 Why does this matter? Let’s consider an example of overharvesting fish populations, which has reduced population sizes and contributed to the loss of unique alleles and genes. Coupled with climate change, this has severely impacted overharvested species’ ability to adapt and recover. In the case of North Atlantic cod, a supergene associated with migratory behavior has been lost from several populations ([Matschiner et al., 2022](https://doi.org/10.1038/s41559-022-01661-x)). This could change the species’ distribution, altering marine ecosystems, and eventually lead to the extinction of the species. -As explained below (see figure), an Ne above 500 (usually a census population size of 5000) **will maintain genetic diversity within populations for a long time.** In other words, **Ne 500** is a “sufficient” size to **prevent loss of genetic diversity within populations**. See [What is a population](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population) for a background on how to define a population in the context of the genetic diversity indicators. +As explained below (see figure), an Ne above 500 (usually a census population size of 5000) **will maintain genetic diversity within populations for a long time.** In other words, **Ne 500** is a “sufficient” size to **prevent loss of genetic diversity within populations**. See [What is a population](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population) for a background on how to define a population in the context of the genetic diversity indicators. Ne below 500 is the approximate point when populations are less able to adapt via natural selection, and start to experience genetic loss. We note that Ne below 50 will lead to very rapid increases in inbreeding, loss of fitness, and changes in the genetic composition of populations, causing high risk of extinction in the short-term. The Ne 500 and Ne 50 thresholds are useful to conservation management and recovery programmes ([Mace et al 2008](https://doi.org/10.1111/j.1523-1739.2008.01044.x)). Because of a need to maintain genetic diversity and adaptive capacity for the long term, the Ne 500 indicator is a key genetic indicator. @@ -21,7 +21,7 @@ Ne below 500 is the approximate point when populations are less able to adapt vi . -The Ne 500 indicator is derived by (a) comparing the **effective population size (Ne) of each population to a critical threshold**, 500, (b) counting the number of populations above the threshold and therefore maintaining genetic diversity, (c) dividing this number by the total number of existing populations since the reporting started to be done (see section [​​Measuring temporal change]8https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change) for why). For example, a species has 5 populations, 3 of which are above Ne 500. The indicator value for this species would be 3/5 = 0.6. For a detailed explanation on calculating the Ne 500 indicator across multiple species see [Hoban et al (2023b)](https://doi.org/10.1111/conl.12953) and [Hoban et al 2023c](https://doi.org/10.32942/X2QK5W), and the [Calculations section](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting) of these guidelines. +The Ne 500 indicator is derived by (a) comparing the **effective population size (Ne) of each population to a critical threshold**, 500, (b) counting the number of populations above the threshold and therefore maintaining genetic diversity, (c) dividing this number by the total number of existing populations since the reporting started to be done (see section [​​Measuring temporal change]8https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change) for why). For example, a species has 5 populations, 3 of which are above Ne 500. The indicator value for this species would be 3/5 = 0.6. For a detailed explanation on calculating the Ne 500 indicator across multiple species see [Hoban et al (2023b)](https://doi.org/10.1111/conl.12953) and [Hoban et al 2023c](https://doi.org/10.32942/X2QK5W), and the [Calculations section](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting) of these guidelines. The values for the Ne 500 indicator range between 0 and 1, with 0 indicating all populations have Ne<500 (no populations are large enough to sustain genetic diversity) and 1 indicating that all populations have Ne>500 (all populations are large enough to sustain genetic diversity). @@ -36,7 +36,7 @@ The values for the Ne 500 indicator range between 0 and 1, with 0 indicating all . -See section [How to estimate Ne?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes) for more details on how to obtain Ne data from genetic or Nc information. +See section [How to estimate Ne?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes) for more details on how to obtain Ne data from genetic or Nc information. -[Previous: Genetic diveristy and indicators](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Genetic_div_indicators.html#genetic-diversity-and-indicators){: .btn .btn-blue .mr-4 } -[Next: Populations maintained indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html#populations-maintained-indicator){: .btn .btn-green } +[Previous: Genetic diveristy and indicators](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Genetic_div_indicators.html#genetic-diversity-and-indicators){: .btn .btn-blue .mr-4 } +[Next: Populations maintained indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html#populations-maintained-indicator){: .btn .btn-green } diff --git a/docs/2_Theoretical_background/PM-indicator.md b/docs/2_Theoretical_background/PM-indicator.md index d2ba518..5d82074 100644 --- a/docs/2_Theoretical_background/PM-indicator.md +++ b/docs/2_Theoretical_background/PM-indicator.md @@ -7,7 +7,7 @@ nav_order: 3 # Populations maintained indicator -In addition to the importance of within population genetic diversity, the diversity between populations is also critical. The populations maintained (PM) indicator measures **the proportion of populations that still exist compared to the total number of populations that used to occur** (i.e., it is a way of quantifying population extinctions). Each population is presumed to be genetically distinct and locally adapted, for example due to harboring genetic variants that are either absent or rare in other populations. Hence loss of any population within a species equates to the loss of genetic diversity/unique genetic adaptations. See [What is a population](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population) for a background on how to define a population in the context of the genetic diversity indicators. This is especially relevant considering the unprecedented rate of environmental change locally and globally; between population diversity provides insurance, enabling the future persistence of a species and the functioning of ecosystems. +In addition to the importance of within population genetic diversity, the diversity between populations is also critical. The populations maintained (PM) indicator measures **the proportion of populations that still exist compared to the total number of populations that used to occur** (i.e., it is a way of quantifying population extinctions). Each population is presumed to be genetically distinct and locally adapted, for example due to harboring genetic variants that are either absent or rare in other populations. Hence loss of any population within a species equates to the loss of genetic diversity/unique genetic adaptations. See [What is a population](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population) for a background on how to define a population in the context of the genetic diversity indicators. This is especially relevant considering the unprecedented rate of environmental change locally and globally; between population diversity provides insurance, enabling the future persistence of a species and the functioning of ecosystems. ![](NewPMindicator_Fig1.png) @@ -15,12 +15,12 @@ In addition to the importance of within population genetic diversity, the divers . -Maintenance of populations is necessary to provide species options for the future and help prevent species collapse. For instance many populations in warmer climatic zones can harbor genetic variants adapted to heat stress, drought, or other related challenges. These populations must be maintained to give the species adaptive capacity for the future. For example, populations of corals have been identified that tolerate much warmer temperatures, and these can help the whole species adapt to warming conditions (by natural migration or human assisted migration). To calculate the indicator, the number of populations currently existing is divided by the number of populations that previously existed. see [How to Guide on Defining Extinct and Extant Populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations). +Maintenance of populations is necessary to provide species options for the future and help prevent species collapse. For instance many populations in warmer climatic zones can harbor genetic variants adapted to heat stress, drought, or other related challenges. These populations must be maintained to give the species adaptive capacity for the future. For example, populations of corals have been identified that tolerate much warmer temperatures, and these can help the whole species adapt to warming conditions (by natural migration or human assisted migration). To calculate the indicator, the number of populations currently existing is divided by the number of populations that previously existed. see [How to Guide on Defining Extinct and Extant Populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations). Like the Ne 500 indicator, values for this indicator range from 0 to 1, with 0 indicating no populations exist (the species is extinct within the country) and 1 indicating that no populations have been lost. As an example, a species was previously known from 4 populations, but only 3 remain (1 has been lost due to extensive habitat transformation/loss). The PM indicator value for this species would be 3/4 = 0.75. -[Previous: Ne 500 indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator){: .btn .btn-blue .mr-4 } -[Next: DNA-based monitoring indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html#dna-based-genetic-monitoring-indicator){: .btn .btn-green } +[Previous: Ne 500 indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator){: .btn .btn-blue .mr-4 } +[Next: DNA-based monitoring indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html#dna-based-genetic-monitoring-indicator){: .btn .btn-green } diff --git a/docs/2_Theoretical_background/What-is-a-population.md b/docs/2_Theoretical_background/What-is-a-population.md index 5bedb97..ec78dd5 100644 --- a/docs/2_Theoretical_background/What-is-a-population.md +++ b/docs/2_Theoretical_background/What-is-a-population.md @@ -13,7 +13,7 @@ Not every occurrence, site or locality is a population; if there is significant The word ‘subpopulation’ may describe clusters of organisms across a landscape (including family units) that are near enough to exchange gene flow. Usually several ‘subpopulations’ are considered together as a population (also called a ‘metapopulation’). When the potential for gene flow is large (e.g., viable tree pollen that can travel tens of kilometers), ‘populations’ can range across large distances, sometimes hundreds of km. -See section [How To Guides](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides) for advice on [How to define populations?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations) +See section [How To Guides](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides) for advice on [How to define populations?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations) {: .important } In IUCN Red List reports the term ‘population’ and ‘subpopulation’ are used differently than intended in here. An ‘IUCN population’ refers to the entire species (i.e., the total number of individuals of the taxon). ‘IUCN subpopulations’ are geographically or otherwise distinct groups of the species between which there is little exchange (IUCN 1995); thus an ‘IUCN subpopulation’ more closely resembles our definition of a ‘population’! @@ -23,5 +23,5 @@ For example, there are two IUCN subpopulations that make up the IUCN population -[Previous: Genetic diversity - advantages](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Gen_div_advantages.html#genetic-diversity---advantages){: .btn .btn-blue .mr-4 } -[Next: Quickstart](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Quickstart/Quickstart.html#quickstart-guide-to-genetic-indicators){: .btn .btn-green } +[Previous: Genetic diversity - advantages](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Gen_div_advantages.html#genetic-diversity---advantages){: .btn .btn-blue .mr-4 } +[Next: Quickstart](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Quickstart/Quickstart.html#quickstart-guide-to-genetic-indicators){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/Extinct_extant_populations.md b/docs/3_Howto_guides_examples/Extinct_extant_populations.md index d8e38c8..87bf153 100644 --- a/docs/3_Howto_guides_examples/Extinct_extant_populations.md +++ b/docs/3_Howto_guides_examples/Extinct_extant_populations.md @@ -22,5 +22,5 @@ Population maintenance can also be evaluated comparing **historical occurrence d ![](Extinct_pop_Fig2.png) ###### **Assessing the PM indicator with occurrence data**. Using occurrence data from herbaria (purple dots) and citizen science (orange dots) of the Mexican mountain juniper, 18 populations were defined, each one considering a mountain or group of mountains isolated by lowlands below 3,000 meters above sea level. Of those, the species has been seen recently in 15 populations (green circles), and these are thus considered extant populations. Two populations can be considered extinct (white crosses), because the species was observed decades ago, but there are no recent observations and extensive land use change has occurred that is seen in satellite photos (this was confirmed by consulting local people). In the last population (white question mark) there are no observations in the last decades, but the habitat remains available according to earth observation data, thus it is uncertain whether the population continues to exist. The point marked with a white “!” lacks accurate geographic information, and thus could belong to any of the nearby mountains, so it was not taken into account to define populations. -[Previous: How to establish a refernce period](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html#how-to-establish-a-reference-period){: .btn .btn-blue .mr-4 } -[Next: How to estimate populaion sizes](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes){: .btn .btn-green } +[Previous: How to establish a refernce period](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html#how-to-establish-a-reference-period){: .btn .btn-blue .mr-4 } +[Next: How to estimate populaion sizes](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/Howto_define_populations.md b/docs/3_Howto_guides_examples/Howto_define_populations.md index 9769ab9..29fa7e9 100644 --- a/docs/3_Howto_guides_examples/Howto_define_populations.md +++ b/docs/3_Howto_guides_examples/Howto_define_populations.md @@ -117,5 +117,5 @@ Metapopulations should represent stable spatial and temporal units. Many species -[Previous: Species list](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list){: .btn .btn-blue .mr-4 } -[Next: How to establish a reference period](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html#how-to-establish-a-reference-period){: .btn .btn-green } +[Previous: Species list](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list){: .btn .btn-blue .mr-4 } +[Next: How to establish a reference period](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html#how-to-establish-a-reference-period){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/Ne_Nc-ratio.md b/docs/3_Howto_guides_examples/Ne_Nc-ratio.md index e43128a..21de020 100644 --- a/docs/3_Howto_guides_examples/Ne_Nc-ratio.md +++ b/docs/3_Howto_guides_examples/Ne_Nc-ratio.md @@ -29,5 +29,5 @@ For example, *Agave* plants can reproduce but sexually and asexually (clones). I -[Previous: How to estimate population sizes](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes){: .btn .btn-blue .mr-4 } -[Next: How to account for uncertainty](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/uncertainty.html){: .btn .btn-green } +[Previous: How to estimate population sizes](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes){: .btn .btn-blue .mr-4 } +[Next: How to account for uncertainty](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/uncertainty.html){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/Populations_sizes.md b/docs/3_Howto_guides_examples/Populations_sizes.md index 2a25b28..09744f0 100644 --- a/docs/3_Howto_guides_examples/Populations_sizes.md +++ b/docs/3_Howto_guides_examples/Populations_sizes.md @@ -7,13 +7,13 @@ nav_order: 4 # How to estimate population sizes -Here we refer to Ne as contemporary effective population size, measuring genetic drift (see also [Glossary](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary) for a more technical definition on Ne and [Background of the Ne 500 indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator)) +Here we refer to Ne as contemporary effective population size, measuring genetic drift (see also [Glossary](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary) for a more technical definition on Ne and [Background of the Ne 500 indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html#ne-500-indicator)) Shortly, the Ne of a population can be obtained in two ways: * **Statistical analysis of DNA sequence data**, when these are available. This will often involve a scientific study where Ne will be estimated and published as part of other genetic diversity summary statistics. -* If genetic data is not available, a simple transformation of **census size** (**Nc; the number of mature individuals) to an Ne using an Ne/Nc ratio is possible.** An Ne/Nc conversion ratio of 0.1 is generally a conservative and suitable ratio to calculate Ne (although typical ratios may range from 0.1 to about 0.3 in many vertebrates and plants - this is a generalization). **By applying a 0.1 Ne/Nc ratio, Ne = 500 translates to a threshold of Nc = 5000** mature individuals. Notice that for species with asexual reproduction (clones) the Nc should be interpreted with care (see below) and section: When the [Ne/Nc ratio](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#nenc-ratio) can’t be used. +* If genetic data is not available, a simple transformation of **census size** (**Nc; the number of mature individuals) to an Ne using an Ne/Nc ratio is possible.** An Ne/Nc conversion ratio of 0.1 is generally a conservative and suitable ratio to calculate Ne (although typical ratios may range from 0.1 to about 0.3 in many vertebrates and plants - this is a generalization). **By applying a 0.1 Ne/Nc ratio, Ne = 500 translates to a threshold of Nc = 5000** mature individuals. Notice that for species with asexual reproduction (clones) the Nc should be interpreted with care (see below) and section: When the [Ne/Nc ratio](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#nenc-ratio) can’t be used. ![](Pop_sizes_Fig1.png) ###### **The effective population size (Ne)** can be obtained by analyzing the genetic diversity of sample of the population, using statistical methods and DNA sequence data. If genetic data is not available, the Ne can be obtained from a simple transformation of the census size (Nc; the number of mature individuals) through the use of an Ne/Nc ratio. @@ -130,6 +130,6 @@ Or the following table extract from the Species Status Assessment Report for Bea ![](Pop_sizes_Fig5.png) -[Previous: Extinct and extant populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations){: .btn .btn-blue .mr-4 } -[Next: How to get the Ne/Nc ratio](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Ne_Nc-ratio.html#how-to-get-the-nenc-ratio){: .btn .btn-green } +[Previous: Extinct and extant populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations){: .btn .btn-blue .mr-4 } +[Next: How to get the Ne/Nc ratio](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Ne_Nc-ratio.html#how-to-get-the-nenc-ratio){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/Reference_period.md b/docs/3_Howto_guides_examples/Reference_period.md index fff8021..94f790a 100644 --- a/docs/3_Howto_guides_examples/Reference_period.md +++ b/docs/3_Howto_guides_examples/Reference_period.md @@ -11,5 +11,5 @@ Because data on the number of existing (extant) and extinct populations is neede Thus, the date range for which the indicators are available is dependent on data availability at the national scale. Typically Nc for the Ne 500 indicator will be obtained from the past decade e.g. post 2010. Going forward it will be reported every 2 to 5 years, typically every 4 years, making it suited to the CBD reporting schedule. As the indicator is increasingly deployed, indicator calculation can be made in temporal windows, including through the use of older biodiversity observation data, reports and consultation with knowledge holders, likely extending indicator assessment at least back to the 1990s. -[Previous: How to define populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations){: .btn .btn-blue .mr-4 } -[Next: Extinct and extant populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations){: .btn .btn-green } +[Previous: How to define populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations){: .btn .btn-blue .mr-4 } +[Next: Extinct and extant populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations){: .btn .btn-green } diff --git a/docs/3_Howto_guides_examples/uncertainty.md b/docs/3_Howto_guides_examples/uncertainty.md index 5f0f9e0..b5f91f6 100644 --- a/docs/3_Howto_guides_examples/uncertainty.md +++ b/docs/3_Howto_guides_examples/uncertainty.md @@ -17,5 +17,5 @@ Some documents may delineate populations in a hierarchical fashion, for example, Another instance when more than one assessment could be done, is when experts or data sources have conflicting results, like a different number of populations. See for example the Monkey example in hard species, or if different studies report Ne based on different genetic markers or statistical methods. -[Previous: How to get the Ne/Nc ratio and when NOT to use it](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Ne_Nc-ratio.html){: .btn .btn-blue .mr-4 } -[Next: Example assessments](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#example-assessments){: .btn .btn-green } \ No newline at end of file +[Previous: How to get the Ne/Nc ratio and when NOT to use it](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Ne_Nc-ratio.html){: .btn .btn-blue .mr-4 } +[Next: Example assessments](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#example-assessments){: .btn .btn-green } \ No newline at end of file diff --git a/docs/3_Quickstart/Quickstart.md b/docs/3_Quickstart/Quickstart.md index 5afd097..d40bf37 100644 --- a/docs/3_Quickstart/Quickstart.md +++ b/docs/3_Quickstart/Quickstart.md @@ -24,54 +24,54 @@ Notice that we have made available a Kobotoolbox form that you can use to gather ### Step 1. Define a species list for which to estimate the indicators -At minimum, 100 species should be evaluated, though ideally many more will be used if capacity is available (e.g. up to 1000). The selection of species should be unbiased. For example, selecting only charismatic species (butterflies, orchids, etc.), species of economic value or rare/ endangered species would result in an indicator that represents the genetic condition of species in that subset rather than all species. Thus the set of species should be as unbiased as possible; this can be achieved by random selection from a list of known, extant species. Analysis and reporting of the indicator may wish to disaggregate for particular subsets e.g. harvested species, pollinators, keystone species, but the overall indicator value should represent all species. See section [Species list](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list) for advice on how to create a species list. +At minimum, 100 species should be evaluated, though ideally many more will be used if capacity is available (e.g. up to 1000). The selection of species should be unbiased. For example, selecting only charismatic species (butterflies, orchids, etc.), species of economic value or rare/ endangered species would result in an indicator that represents the genetic condition of species in that subset rather than all species. Thus the set of species should be as unbiased as possible; this can be achieved by random selection from a list of known, extant species. Analysis and reporting of the indicator may wish to disaggregate for particular subsets e.g. harvested species, pollinators, keystone species, but the overall indicator value should represent all species. See section [Species list](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list) for advice on how to create a species list. ## Gather data ### Step 2: Define population boundaries in geographic space -For each focal species it is first necessary to define ‘populations’. Many local and national biodiversity monitoring programs (e.g. at species or ecosystem level) have already defined populations, or it may be straightforward to define them based on geographic isolation, occupying distinct habitats or ecoregions, association with a geographic feature like a mountain range or lake, etc. The goal is to have a discrete count, e.g. 4 populations. However, the indicator can accommodate uncertainty, such that different numbers of populations may be assumed. Full guidance on defining populations for a wide variety of organisms are provided in the [How to define populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations) section. See also. [What is a population?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer) in the background section. +For each focal species it is first necessary to define ‘populations’. Many local and national biodiversity monitoring programs (e.g. at species or ecosystem level) have already defined populations, or it may be straightforward to define them based on geographic isolation, occupying distinct habitats or ecoregions, association with a geographic feature like a mountain range or lake, etc. The goal is to have a discrete count, e.g. 4 populations. However, the indicator can accommodate uncertainty, such that different numbers of populations may be assumed. Full guidance on defining populations for a wide variety of organisms are provided in the [How to define populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_define_populations.html#how-to-define-populations) section. See also. [What is a population?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer) in the background section. ### Step 3. Count the number of extant and extinct populations -Once population boundaries have been defined, it is necessary to count how many populations currently exist (extant populations) and, if possible, count the number of populations that have been lost (extinct populations). This data will be used to estimate the PM indicator. See section [How to count extant and extinct populations?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations) for details and notes on the reference period. +Once population boundaries have been defined, it is necessary to count how many populations currently exist (extant populations) and, if possible, count the number of populations that have been lost (extinct populations). This data will be used to estimate the PM indicator. See section [How to count extant and extinct populations?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Extinct_extant_populations.html#extinct-and-extant-populations) for details and notes on the reference period. {: .note } Note: If it is not possible to calculate the number of extinct populations, **it is still possible to proceed** to the next step (the Ne 500 indicator). ### Step 4. Compile data on census size (Nc) or effective population size (Ne) -After defining populations, it is necessary to collect data on census population sizes (Nc) or, if available, Ne estimated from genetic data. Many biodiversity monitoring programs for priority species will have Nc data available - in some cases in a centralized national database, while in other cases, it may be scattered among different national reports, assessments, and other knowledge. "Other knowledge" should be considered broadly and it includes citizen science, local knowledge, indigenous knowledge, and informal data held by small NGOs and similar groups. Ne estimated from genetic data is less frequent, but it is already available for hundreds of species globally. See [Data sources](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#data-sources) in the Data collection section. +After defining populations, it is necessary to collect data on census population sizes (Nc) or, if available, Ne estimated from genetic data. Many biodiversity monitoring programs for priority species will have Nc data available - in some cases in a centralized national database, while in other cases, it may be scattered among different national reports, assessments, and other knowledge. "Other knowledge" should be considered broadly and it includes citizen science, local knowledge, indigenous knowledge, and informal data held by small NGOs and similar groups. Ne estimated from genetic data is less frequent, but it is already available for hundreds of species globally. See [Data sources](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#data-sources) in the Data collection section. ### Step 5: For populations with Nc data, calculate Ne based on an Ne:Nc ratio (skip if you obtained Ne directly from a genetic study) -To convert Nc to Ne it is important to choose a ratio of effective-to-census size and then multiplying the population’s census size by this ratio to obtain the population’s effective size. As mentioned in the [Ne 500 indicator background](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/2_Theoretical_background/Ne-500.md#ne-500-indicator) the default ratio, which is slightly conservative, is 1/10th or 0.1 (thus the minimum Nc would be 5000). Alternatively, a taxon-specific ratio can be obtained several ways. See How to estimate population sizes? in the How to guides. To incorporate uncertainty in calculations, the calculation can be repeated using multiple Ne/Nc ratios. But it is acceptable and useful to use the well-recognized 0.1 ratio. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. +To convert Nc to Ne it is important to choose a ratio of effective-to-census size and then multiplying the population’s census size by this ratio to obtain the population’s effective size. As mentioned in the [Ne 500 indicator background](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/2_Theoretical_background/Ne-500.md#ne-500-indicator) the default ratio, which is slightly conservative, is 1/10th or 0.1 (thus the minimum Nc would be 5000). Alternatively, a taxon-specific ratio can be obtained several ways. See How to estimate population sizes? in the How to guides. To incorporate uncertainty in calculations, the calculation can be repeated using multiple Ne/Nc ratios. But it is acceptable and useful to use the well-recognized 0.1 ratio. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. ## Use data to calculate indicators ### Step 6. Calculate the proportion of maintained populations (PM indicator) -For each species, divide the number of populations currently existing (“extant populations”) by the number of populations that previously existed (“extinct populations”). Values for this indicator range from 0 to 1, with 0 indicating no populations exist (the species is extinct within the country) and 1 indicating that no populations have been lost. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. +For each species, divide the number of populations currently existing (“extant populations”) by the number of populations that previously existed (“extinct populations”). Values for this indicator range from 0 to 1, with 0 indicating no populations exist (the species is extinct within the country) and 1 indicating that no populations have been lost. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. ### Step 7: Calculate the proportion of populations above the 500 Ne threshold (Ne 500 indicator) -For each species, divide the number of populations with Ne above 500 by the total number of populations. The indicator is then the proportion (from 0 to 1) of all populations that are above 500. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. +For each species, divide the number of populations with Ne above 500 by the total number of populations. The indicator is then the proportion (from 0 to 1) of all populations that are above 500. See section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting) for details, [equations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations) and [R scripts](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the calculations. ### Step 8. Indicators summary and reports -To combine the indicator values across species in a given country or geographic location, a simple average of the proportion for all the relevant species should be performed. If taxonomic groups are not represented evenly, the indicator value is the mean of each taxonomic group’s means, which down-weights overly represented taxonomic groups, e.g. mammals. Additionally, each species can be weighted by the proportion of its geographic range in the country, from 0 to 1, to reflect national responsibility, with full weight for endemic species. Transboundary/ transnational populations can be weighted similarly (e.g. by the proportion of that population falling within the Parties borders). The indicator would range between 0 and 1 (with 1 being the desired state - all populations above an effective size of 500). In addition, subsets of the indicator can be calculated for different species types e.g. pollinators, threatened species, etc., by repeating indicator calculations for only species in that type. Equations for indicator calculation are given in [Hoban et al (2023b)](https://doi.org/10.1111/conl.12953) and section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting). See also [R scripts](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the summary and reports. +To combine the indicator values across species in a given country or geographic location, a simple average of the proportion for all the relevant species should be performed. If taxonomic groups are not represented evenly, the indicator value is the mean of each taxonomic group’s means, which down-weights overly represented taxonomic groups, e.g. mammals. Additionally, each species can be weighted by the proportion of its geographic range in the country, from 0 to 1, to reflect national responsibility, with full weight for endemic species. Transboundary/ transnational populations can be weighted similarly (e.g. by the proportion of that population falling within the Parties borders). The indicator would range between 0 and 1 (with 1 being the desired state - all populations above an effective size of 500). In addition, subsets of the indicator can be calculated for different species types e.g. pollinators, threatened species, etc., by repeating indicator calculations for only species in that type. Equations for indicator calculation are given in [Hoban et al (2023b)](https://doi.org/10.1111/conl.12953) and section [Calculations and reporting](https://github.com/AliciaMstt/guidelines-genetic-diversity-indicators/blob/main/docs/6_Calculations_and_reporting/Calculations_and_reporting.md#calculations-and-reporting). See also [R scripts](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) to help with the summary and reports. ## Use data to measure change and for management decisions ### Step 9: Measure temporal change in the indicators -Temporal change can be calculated using multiple time point values of the indicators. For the Ne 500 indicator, any population that goes extinct after the country’s baseline year (each country is directed by the CBD in the [monitoring framework](https://www.cbd.int/doc/decisions/cop-15/cop-15-dec-05-en.pdf) to choose a baseline, which defaults to 2010-2020 but which may be adjusted to country context) is assigned an Ne of 0 and are therefore below Ne 500. These populations must be retained in the calculation in order to avoid the perverse incentive to “raise” the indicator value through population extinction. See [Measure temporal change](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change) for details and other considerations. +Temporal change can be calculated using multiple time point values of the indicators. For the Ne 500 indicator, any population that goes extinct after the country’s baseline year (each country is directed by the CBD in the [monitoring framework](https://www.cbd.int/doc/decisions/cop-15/cop-15-dec-05-en.pdf) to choose a baseline, which defaults to 2010-2020 but which may be adjusted to country context) is assigned an Ne of 0 and are therefore below Ne 500. These populations must be retained in the calculation in order to avoid the perverse incentive to “raise” the indicator value through population extinction. See [Measure temporal change](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change) for details and other considerations. ### Step 10. Management based on the indicators The indicators are designed for use in practical biodiversity management – not just for reporting to the CBD. For example, either indicator value at a single time point or over time can be used for: raising alarm in regions or taxonomic groups with low indicator values, prioritizing which species and populations are most in need of management to halt genetic erosion, designing management strategies and goals (e.g. reintroduction, population supplementation to increase Ne), tracking the consequences or effectiveness of management (e.g. if the indicator value improves), and communicating to the public about genetic diversity conservation. -[Previous: Background](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background){: .btn .btn-blue .mr-4 } -[Next: Species list](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list){: .btn .btn-green } +[Previous: Background](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background){: .btn .btn-blue .mr-4 } +[Next: Species list](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4_Species_list/Species_list.html#species-list){: .btn .btn-green } diff --git a/docs/4_Species_list/Species_list.md b/docs/4_Species_list/Species_list.md index c82c2b1..6d6bcf6 100644 --- a/docs/4_Species_list/Species_list.md +++ b/docs/4_Species_list/Species_list.md @@ -63,5 +63,5 @@ It is important to fill in the Kobo form for every species on the 100+ species l ![](New_Species_list_Fig1.png) ###### **Conceptual illustration of the fact that each country will evaluate >100 species**, and that some proportion of species evaluated will have insufficient data for calculation of the indicators. The proportion of X/(X+Y) may (possibly, but not necessarily) suggest some groups or countries that consistently have limited data for calculating indicators. -[Previous: Quickstart](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Quickstart/Quickstart.html#quickstart-guide-to-genetic-indicators){: .btn .btn-blue .mr-4 } -[Next: How to - guides](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides){: .btn .btn-green } +[Previous: Quickstart](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Quickstart/Quickstart.html#quickstart-guide-to-genetic-indicators){: .btn .btn-blue .mr-4 } +[Next: How to - guides](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides){: .btn .btn-green } diff --git a/docs/4b_Example_assessments/Example_assessments.md b/docs/4b_Example_assessments/Example_assessments.md index abfa4b2..e0a3fc8 100644 --- a/docs/4b_Example_assessments/Example_assessments.md +++ b/docs/4b_Example_assessments/Example_assessments.md @@ -96,5 +96,5 @@ A genetic study would be good to assess connectivity and genetic distinctness. M **How we dealt with it:** Habitat mapping could help define potential habitat boundaries and population boundaries better than with the observation data alone. We pruned observations to know sites in the northern part of the country, and considered the southern part to a great extent as a single metapopulation. -[Previous: How to - guides](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides){: .btn .btn-blue .mr-4 } -[Next: Data collection](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection){: .btn .btn-green } +[Previous: How to - guides](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Howto_guides_examples.html#how-to---guides){: .btn .btn-blue .mr-4 } +[Next: Data collection](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection){: .btn .btn-green } diff --git a/docs/5_Data_collection/Data_sources.md b/docs/5_Data_collection/Data_sources.md index 7f0386b..0f8579c 100644 --- a/docs/5_Data_collection/Data_sources.md +++ b/docs/5_Data_collection/Data_sources.md @@ -11,9 +11,9 @@ nav_order: 1 The amount of time and effort for collection of data will vary depending on the country and data source. There are roughly three categories of data sources: -(1) *automated*: Data from a centralized inventory of multiple to many species. Some countries may have a centralized database of many species (across taxonomic groups and levels of rarity) from which estimates of population sizes and counts of the number of populations can be extracted directly and quickly. This may be especially the case for plants, long lived organisms, and those of high economic, ecological, conservation or cultural value. Extracting data directly from computer files or tables is sometimes very straightforward and automatable (Figure [Process to identify data from different sources](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#process-to-identify-data-from-different-sources-manual-expert-automated-to-assess-genetic-indicators-for-a-set-of-species-adapted-from-hoban-et-al-2023)). +(1) *automated*: Data from a centralized inventory of multiple to many species. Some countries may have a centralized database of many species (across taxonomic groups and levels of rarity) from which estimates of population sizes and counts of the number of populations can be extracted directly and quickly. This may be especially the case for plants, long lived organisms, and those of high economic, ecological, conservation or cultural value. Extracting data directly from computer files or tables is sometimes very straightforward and automatable (Figure [Process to identify data from different sources](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#process-to-identify-data-from-different-sources-manual-expert-automated-to-assess-genetic-indicators-for-a-set-of-species-adapted-from-hoban-et-al-2023)). -(2) *manual*: Collection of data for each species from various sources. For many countries, we anticipate that data will need to be extracted manually by humans by reading reports, websites, planning documents, and/or expert consultation and extracting the quantification of populations maintained and population sizes ([Figure Process to identify data from different sources](ttps://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#process-to-identify-data-from-different-sources-manual-expert-automated-to-assess-genetic-indicators-for-a-set-of-species-adapted-from-hoban-et-al-2023)). One source may suffice (e.g. a comprehensive report), while sometimes it may be necessary to consult more than one resource. +(2) *manual*: Collection of data for each species from various sources. For many countries, we anticipate that data will need to be extracted manually by humans by reading reports, websites, planning documents, and/or expert consultation and extracting the quantification of populations maintained and population sizes ([Figure Process to identify data from different sources](ttps://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#process-to-identify-data-from-different-sources-manual-expert-automated-to-assess-genetic-indicators-for-a-set-of-species-adapted-from-hoban-et-al-2023)). One source may suffice (e.g. a comprehensive report), while sometimes it may be necessary to consult more than one resource. (3) *expert*: Local communities or experts consultation. For some species or regions, it will be most appropriate to consult people from local communities, staff from conservation initiatives (e.g. park rangers), or other stakeholders who know the species within their territories. The goal is to gather knowledge that is current but may not be published or written, but is known, including if possible with measures of uncertainty. Forming a panel or workshop of knowledge holders in a particular taxonomic group (e.g. amphibians, trees, etc.) also can be an efficient way to gather data on dozens of species in a short period of time. @@ -36,5 +36,5 @@ Below are some example data sources: If collecting data from a written source, each data source should be read thoroughly. Red List assessments and management plans might be 1 to 20 pages long (sometimes longer), and some reports on well studied species may exceed 100 pages. The text might clearly state the size of each population, with text, tables, or maps. However, data may be incomplete, such as listing the size of only the largest or smallest populations. As noted above, it is ok to submit species for which some information is missing (see common Issues below). The time necessary to gather data from individual sources (and/or consult experts) may range from 45 minutes (for clear, short reports), to 5+ hours. -[Previous: Example assessments](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#example-assessments){: .btn .btn-blue .mr-4 } -[Next: Web-tool for data collection](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Web_tool.html#web-tool-for-data-collection-kobo){: .btn .btn-green } +[Previous: Example assessments](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#example-assessments){: .btn .btn-blue .mr-4 } +[Next: Web-tool for data collection](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Web_tool.html#web-tool-for-data-collection-kobo){: .btn .btn-green } diff --git a/docs/5_Data_collection/Kobo_toolbox_help.md b/docs/5_Data_collection/Kobo_toolbox_help.md index d9b022c..e19ea22 100644 --- a/docs/5_Data_collection/Kobo_toolbox_help.md +++ b/docs/5_Data_collection/Kobo_toolbox_help.md @@ -37,7 +37,7 @@ The R processing scripts and functions described in this guidelines assume that The variables names in the exported data match the "name" column in the [kobo_form.xlsx](https://github.com/AliciaMstt/GeneticIndicators/raw/main/kobo_form.xlsx) survey tab. In the same file, you can check the question of the form it refers to in the "label" tab. -See section [R scripts for calculation and reporting](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) for scripts to process the Kobotoolbox output data and calculate the genetic diversity indicators. +See section [R scripts for calculation and reporting](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting) for scripts to process the Kobotoolbox output data and calculate the genetic diversity indicators. -[Previous: Web-tool for data collection](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Web_tool.html#web-tool-for-data-collection-kobo){: .btn .btn-blue .mr-4 } -[Next: Recommended data and variables for calculating indicators](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Recommended_data.html#recommended-minimum-data-and-metadata-variables-for-calculating-genetic-diversity-indicators){: .btn .btn-green } +[Previous: Web-tool for data collection](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Web_tool.html#web-tool-for-data-collection-kobo){: .btn .btn-blue .mr-4 } +[Next: Recommended data and variables for calculating indicators](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Recommended_data.html#recommended-minimum-data-and-metadata-variables-for-calculating-genetic-diversity-indicators){: .btn .btn-green } diff --git a/docs/5_Data_collection/Recommended_data.md b/docs/5_Data_collection/Recommended_data.md index 51661c9..ff2beed 100644 --- a/docs/5_Data_collection/Recommended_data.md +++ b/docs/5_Data_collection/Recommended_data.md @@ -48,8 +48,8 @@ table th:nth-of-type(5) { | **Population size data for Ne 500 indicator** | | | | | | | Population id unique within the species (automatically generated if using Kobo) | Character text | pop1 | population | | | Point estimate of the Ne of the population, if available from genetic data | decimal | 320 | Ne | -| | The range of the population census size, if the population size type selected is Nc_range. See “Quantitative range or qualitative estimates” in [How to get the Nc?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc) | Categorical | less_5000_bymuch | NcRange | -| | NcRange values transformed to numeric values, if NcRange was provided. (See “Quantitative range or qualitative estimates” in [How to get the Nc?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc)) Single Nc value for analysis, estimated from NcRange values. NcRange values can be converted into a single number using the following guidelines: If NcRange is 'more than 5000 by much', Nc_from_range = 10000; 'more than 5000' = 5500; 'range includes 5000 = 5001; 'less than 5000' = 4050; 'less than 5000 by much' = 500 | Integer | 5500 | Nc_from_range | +| | The range of the population census size, if the population size type selected is Nc_range. See “Quantitative range or qualitative estimates” in [How to get the Nc?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc) | Categorical | less_5000_bymuch | NcRange | +| | NcRange values transformed to numeric values, if NcRange was provided. (See “Quantitative range or qualitative estimates” in [How to get the Nc?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc)) Single Nc value for analysis, estimated from NcRange values. NcRange values can be converted into a single number using the following guidelines: If NcRange is 'more than 5000 by much', Nc_from_range = 10000; 'more than 5000' = 5500; 'range includes 5000 = 5001; 'less than 5000' = 4050; 'less than 5000 by much' = 500 | Integer | 5500 | Nc_from_range | | | Ne estimate based on Nc, if Nc was provided. Calculated by multiplying Nc by a ratio (0.1 default or other) | Numeric | 300 | Ne_from_Nc | | | Single Ne estimated used for analysis for this population. Ne from genetic data has preference. If not available, Ne_from_Nc can be used. | Numeric | 320 | Ne_combined | | **DNA-based monitoring indicator** | | | | | @@ -73,7 +73,7 @@ table th:nth-of-type(5) { | | Source of species population information (literature reference, website link, expert consultation). If more than once source was used, they are separated by semicolon ";" | Character text | Mastretta-Yanes, A., Wegier, A., Vázquez-Lobo, A., & Piñero, D. (2012). Distinctiveness, rarity and conservation in a subtropical highland conifer. Conservation Genetics, 13(1), 211–222. https://doi.org/10.1007/s10592-011-0277-y ; Moreno-Letelier, A., Mastretta-Yanes, A., & Barraclough, T. G. (2014). Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: Clues for the diversification of North American conifers. New Phytologist, 203(1), 335–347. https://doi.org/10.1111/nph.12761 ; Experts Socorro González-Elizondo and Alicia Mastretta-Yanes; https://enciclovida.mx/especies/155216-juniperus-blancoi | source_populations | | **Pop size for Ne 500** | | | | | | | Population name | text | Gironde | name | -| | Whether the population is historically natural or was introduced, re-introduced or reinforced. See [Glossary](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary). | Categorical | reinforced | Origin | +| | Whether the population is historically natural or was introduced, re-introduced or reinforced. See [Glossary](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary). | Categorical | reinforced | Origin | | | If the population was introduced, re-introduced or reinforced, year or years in which this was done. | text | 1995; 2007; 2008; 2009; 2010; 2011; 2012; 2013; 2014 | IntroductionYear | | | Lower limit of the Ne confidence interval for the population, if available. | decimal | 238 | NeLower | | | Upper limit of the Ne confidence interval for the population, if available. | decimal | 405 | NeUpper | @@ -83,8 +83,8 @@ table th:nth-of-type(5) { | | References of all relevant sources reporting on effective population size for the population. Separated by a semicolon (;). | text | daSilva&Tolley 2018. Conservation genetics of an endemic and threatened amphibian (Capensibufo rosei): a leap towards establishing a genetic monitoring framework. Conservation genetics 19:349-363. doi: 10.1007/s10592-017-1008-9 | SourceNe | | | Whether the census population size (Nc) is a point or range estimate for the population | character text | Nc_point | NcType | | | Year or years in which the Nc was estimated for the population (year when the sampling was done, not when it was published) | text | 2010 | NcYear | -| | Method to calculate Nc for the population. See options in [How to estimate Nc?](8https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc) | Categorical | Nc_method_count | NcMethod | -| | The point estimate of the population size, if the population size type selected is Nc_point. See “Point estimates in [How to get the Nc?](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc)” | Integer | 2168 | NcPoint | +| | Method to calculate Nc for the population. See options in [How to estimate Nc?](8https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc) | Categorical | Nc_method_count | NcMethod | +| | The point estimate of the population size, if the population size type selected is Nc_point. See “Point estimates in [How to get the Nc?](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-get-the-nc)” | Integer | 2168 | NcPoint | | | The lower limit of the point estimate of the population size, if the population size type (Nc_type_pop*) selected is Nc_point. | Integer | 2040 | NcLower | | | The upper limit of the point estimate of the population size, if the population size type (Nc_type_pop*) selected is Nc_point. | Integer | 2312 | NcUpper | | | References of all relevant sources reporting on census population size for each population. Separated by a semicolon (;). | Character text | Becker, F. 2017. Estimating the Population Size of a Rare and Elusive Species: the Case of Roses Mountain Toadlet. MSc thesis. University of Cape Town. | SourceNc | @@ -109,5 +109,5 @@ table th:nth-of-type(5) { {: .note } Other useful metadata include the realm (terrestrial, aquatic, marine), and ecosystem (e.g. rainforest), as well as threat status. These are not required, but they are useful to disaggregate the indicators. -[Previous: KoboToolBox help](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help){: .btn .btn-blue .mr-4 } -[Next: Calculations and reporting](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting){: .btn .btn-green } +[Previous: KoboToolBox help](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help){: .btn .btn-blue .mr-4 } +[Next: Calculations and reporting](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting){: .btn .btn-green } diff --git a/docs/5_Data_collection/Web_tool.md b/docs/5_Data_collection/Web_tool.md index 595b9d3..ca16f09 100644 --- a/docs/5_Data_collection/Web_tool.md +++ b/docs/5_Data_collection/Web_tool.md @@ -9,7 +9,7 @@ nav_order: 2 During the first multinational pilot on the genetic diversity indicators we agreed on a set of variables and species information needed to estimate the genetic diversity indicators. To facilitate collecting data in a **reproducible and standardized way**, we built a web-form for data entry using KoboToolBox. -KoboToolBox ([https://www.kobotoolbox.org/](https://www.kobotoolbox.org/)) is a data collection tool with some useful features to prevent common human errors and facilitate decisions for the user. It records data to Kobo's free servers for research or humanitarian purposes, but it can also be installed at institutional servers. Regardless of the server, Kobo is not meant for long-term storage of data, since it is a data collection tool, not a database itself. You **may** wish to use it for indicator data collection because it is an open software tool that anyone can use to create their own project, administer their own teams (ie. group of users with access to a survey either to see it, edit the questions, collect data, or see the data) and collect data. The questions of a form can also be shared for others to use or adapt in their own project. You can learn more about KoboToolBox as a tool in the section [KoboToolBox help](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help). +KoboToolBox ([https://www.kobotoolbox.org/](https://www.kobotoolbox.org/)) is a data collection tool with some useful features to prevent common human errors and facilitate decisions for the user. It records data to Kobo's free servers for research or humanitarian purposes, but it can also be installed at institutional servers. Regardless of the server, Kobo is not meant for long-term storage of data, since it is a data collection tool, not a database itself. You **may** wish to use it for indicator data collection because it is an open software tool that anyone can use to create their own project, administer their own teams (ie. group of users with access to a survey either to see it, edit the questions, collect data, or see the data) and collect data. The questions of a form can also be shared for others to use or adapt in their own project. You can learn more about KoboToolBox as a tool in the section [KoboToolBox help](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help). **Show me the web-form!** @@ -17,5 +17,5 @@ You can see a **dummy example** of how the online form looks once it is deployed -[Previous: Data sources](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#data-sources){: .btn .btn-blue .mr-4 } -[Next: KoboToolBox help](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help){: .btn .btn-green } +[Previous: Data sources](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_sources.html#data-sources){: .btn .btn-blue .mr-4 } +[Next: KoboToolBox help](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Kobo_toolbox_help.html#kobotoolbox-help){: .btn .btn-green } diff --git a/docs/6_Calculations_and_reporting/Country_ind_values.md b/docs/6_Calculations_and_reporting/Country_ind_values.md index 9f33ea3..bd4c459 100644 --- a/docs/6_Calculations_and_reporting/Country_ind_values.md +++ b/docs/6_Calculations_and_reporting/Country_ind_values.md @@ -46,5 +46,5 @@ The next result shows the actual indicator values calculated for more than 900 s ##### *Figure. Example of aggregated indicator values*. Proportion of populations with Ne>500 for animals, plants and other taxonomic groups for more than 900 species in 9 countries. Made with data from [Mastretta-Yanes et al (2024)](https://ecoevorxiv.org/repository/view/6104/). -[Previous: Equations and example calculations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations){: .btn .btn-blue .mr-4 } -[Next: Measuring temporal change](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change){: .btn .btn-green } +[Previous: Equations and example calculations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Equations.html#equations-and-example-calculations){: .btn .btn-blue .mr-4 } +[Next: Measuring temporal change](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change){: .btn .btn-green } diff --git a/docs/6_Calculations_and_reporting/Equations.md b/docs/6_Calculations_and_reporting/Equations.md index bf9faee..584656e 100644 --- a/docs/6_Calculations_and_reporting/Equations.md +++ b/docs/6_Calculations_and_reporting/Equations.md @@ -29,7 +29,7 @@ table th:nth-of-type(3) { | Ne > 500 Indicator | Populations Maintained (PM) Indicator | Number of species being monitored using DNA-based methods | |:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------------------------------------------------:| -| Proportion of populations with an effective population size (Ne) greater than 500.

![](equation_Ne500ind.png)

**Note:** When Ne is unavailable, [measures of Nc can be used to estimate Ne](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html).
0.1 Ne/Nc conversion ratio is recommended if unknown. | Proportion of populations within a species that are maintained (i.e., extant populations) compared to the total number known (i.e., extant + extinct).

![](equation_PMind.png)

N is the number of extant or extinct populations within a species. **Note:** A [See How to establish a reference period to estimate extinct populations](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html) | A count of the number of species where at least one population is being genetically (temporally) monitored with DNA-based methods | +| Proportion of populations with an effective population size (Ne) greater than 500.

![](equation_Ne500ind.png)

**Note:** When Ne is unavailable, [measures of Nc can be used to estimate Ne](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html).
0.1 Ne/Nc conversion ratio is recommended if unknown. | Proportion of populations within a species that are maintained (i.e., extant populations) compared to the total number known (i.e., extant + extinct).

![](equation_PMind.png)

N is the number of extant or extinct populations within a species. **Note:** A [See How to establish a reference period to estimate extinct populations](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Reference_period.html) | A count of the number of species where at least one population is being genetically (temporally) monitored with DNA-based methods | For instance, in the example of hypothetical populations of fish (Figure. [Illustration of genetic diversity indicators for hypothetical populations](#illustration-of-genetic-diversity-indicators-for-hypothetical-populations-four-hypothetical-fish-populations-occur-within-a-country-one-fish--1000-mature-fishes-colors-show-genetic-diversity-in-the-year-the-indicators-were-assessed-1-population-is-extinct-lost-and-only-one-is-large-enough-ne--500-to-retain-genetic-diversity)). Three of four historical populations are maintained, so the PM indicator is 3/4=0.75. Only one of the remaining populations is has an Ne >500, so the Ne 500 indicator is ⅓ = 0.33. DNA-based methods have not been used to monitor genetic diversity, so the DNA-based monitoring indicator is 0. @@ -37,5 +37,5 @@ For instance, in the example of hypothetical populations of fish (Figure. [Illus ##### **Illustration of genetic diversity indicators for hypothetical populations**. Four hypothetical fish populations occur within a country. One fish = 1000 mature fishes. Colors show genetic diversity. In the year the indicators were assessed, 1 population is extinct (lost), and only one is large enough (Ne > 500) to retain genetic diversity. -[Previous: Data collection](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection){: .btn .btn-blue .mr-4 } -[Next: Calculating country indicator values](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Country_ind_values.html#calculating-country-indicator-values){: .btn .btn-green } +[Previous: Data collection](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/5_Data_collection/Data_collection.html#data-collection){: .btn .btn-blue .mr-4 } +[Next: Calculating country indicator values](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Country_ind_values.html#calculating-country-indicator-values){: .btn .btn-green } diff --git a/docs/6_Calculations_and_reporting/R_scripts.md b/docs/6_Calculations_and_reporting/R_scripts.md index b0cf878..6e351e5 100644 --- a/docs/6_Calculations_and_reporting/R_scripts.md +++ b/docs/6_Calculations_and_reporting/R_scripts.md @@ -17,7 +17,7 @@ While manual calculation is certainly possible (e.g., using Excel), we have crea The following R functions take as input a data frame with the data downloaded from the Kobo form and **extract and format the data** in order to estimate each of the Genetic Diversity Indicators. -See examples of the input and output data frames in the "Estimating indicator…" sections below. And see the notebook [quality check](https://aliciamstt.github.io/GeneticIndicators/1_quality_check.html) and [cleaning for the multinational pilot assessment](https://aliciamstt.github.io/GeneticIndicators/2_cleaning.html), and [section 4](https://aliciamstt.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) of this [repository](https://github.com/AliciaMstt/GeneticIndicators) for detailed examples of how these functions were used as part of a pipeline. +See examples of the input and output data frames in the "Estimating indicator…" sections below. And see the notebook [quality check](https://ccgenetics.github.io/GeneticIndicators/1_quality_check.html) and [cleaning for the multinational pilot assessment](https://ccgenetics.github.io/GeneticIndicators/2_cleaning.html), and [section 4](https://ccgenetics.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) of this [repository](https://github.com/AliciaMstt/GeneticIndicators) for detailed examples of how these functions were used as part of a pipeline. Functions: @@ -161,7 +161,7 @@ table th:nth-of-type(7) { |0586b61e-7805-42d7-84e1-dd8a6983c941 |Bombina variegata |Belgium | 12| 12| 0| 0| |065a53ba-051b-440c-a189-9a3c47d02571 |Caracal caracal |South Africa | 1| 1| 0| 0| -See the notebook of the [analyses and figures for the multinational pilot assessment](https://aliciamstt.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://aliciamstt.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. +See the notebook of the [analyses and figures for the multinational pilot assessment](https://ccgenetics.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://ccgenetics.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. ### Estimate the PM indicator @@ -205,7 +205,7 @@ Output selecting the most relevant columns: |France |Taxus baccata | 1| NA| NA| |France |Angelica heterocarpa | 4| NA| NA| -See the n[otebook of the analyses and figures for the multinational assessment](https://aliciamstt.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://aliciamstt.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. +See the n[otebook of the analyses and figures for the multinational assessment](https://ccgenetics.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://ccgenetics.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. ### Estimate the genetic monitoring indicator @@ -253,7 +253,7 @@ The output is the number of taxa with genetic monitoring per country (or per any |sweden | 20| |united\_states | 6| -See the n[otebook of the analyses and figures for the multinational assessment](https://aliciamstt.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://aliciamstt.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. +See the n[otebook of the analyses and figures for the multinational assessment](https://ccgenetics.github.io/GeneticIndicators/3_manuscript_figures_analyses.html#estimate-indicators) and [section 4 of this README](https://ccgenetics.github.io/GeneticIndicators/#4-pipeline-used-in-the-multinational-assessment) for detailed examples of how these functions were used as part of a pipeline. ### Dependencies @@ -266,5 +266,5 @@ Functions were developed and tested using: If you are getting a message with something like "**Error in `mutate()`** ... **Caused by error in `na_if()`:**" it is likely because you have a different version of dplyr or tidyr than above. -[Previous: Measuring temporal change](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change){: .btn .btn-blue .mr-4 } -[Next: Glossary](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary){: .btn .btn-green } +[Previous: Measuring temporal change](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Temporal_change.html#measuring-temporal-change){: .btn .btn-blue .mr-4 } +[Next: Glossary](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary){: .btn .btn-green } diff --git a/docs/6_Calculations_and_reporting/Temporal_change.md b/docs/6_Calculations_and_reporting/Temporal_change.md index b88a5d2..98528bf 100644 --- a/docs/6_Calculations_and_reporting/Temporal_change.md +++ b/docs/6_Calculations_and_reporting/Temporal_change.md @@ -22,5 +22,5 @@ In addition, it is anticipated that biodiversity monitoring capacity within coun Temporal increases in the proportion of populations with Ne above 500 would indicate improvement in the maintenance of genetic diversity (on average slowing the rate of genetic erosion and eventually ‘bending the curve’ such that genetic diversity is restored via natural processes of mutation, migration, etc.). Decreases would indicate worsening status (accelerating rate of genetic erosion). Static values would indicate a stable state of the indicator (stable rate of genetic erosion - though not necessarily a halting of genetic erosion - it is only halted when Ne >500). The indicator is designed to be recalculated as new data are compiled, which in many species is a timescale of 2 to 5 years, thus the indicator would be calculated and reported on typically once every 4 years (fitting the timespan of CBD reporting). -[Previous: Calculating country indicators values](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Country_ind_values.html#calculating-country-indicator-values){: .btn .btn-blue .mr-4 } -[Next: R scripts for calculation and reporting](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting){: .btn .btn-green } +[Previous: Calculating country indicators values](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Country_ind_values.html#calculating-country-indicator-values){: .btn .btn-blue .mr-4 } +[Next: R scripts for calculation and reporting](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/R_scripts.html#r-scripts-for-calculation-and-reporting){: .btn .btn-green } diff --git a/docs/7_Glossary/Glossary.md b/docs/7_Glossary/Glossary.md index e2f5e51..340fa8c 100644 --- a/docs/7_Glossary/Glossary.md +++ b/docs/7_Glossary/Glossary.md @@ -23,7 +23,7 @@ has_children: false The number of reproductively mature individuals in a population. This number can be estimated via physical counts- Itt should be noted that these counts are not necessarily exact numbers of individuals, but rather estimates given that the detection probability is dependent on several factors, including population density, observer effort (time), and experience. There are instances where it is impractical or impossible to estimate the size of a population by traditional counting methods. In such instances, additional methods, such as capture-mark-recapture, can be used. An estimate based on density in a given unit area and the total area can be used, if it can be assumed that the area is occupied. Estimates can also be made by local knowledge holders based on personal experience. ### Effective population size, Ne -The effective population size is the genetic complement of **census size**; where census size influences ecological aspects of a population, genetic factors of a population are influenced by Ne. Both random [allele](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#allele) frequency change and estimates of inbreeding are influenced by Ne. For the purposes of the genetic diversity indicators, Ne refers to contemporary effective population size which measures ongoing and near-term genetic drift. Estimating contemporary Ne does not require knowing mutation rates (which is required for estimating historic Ne), but does require genetic data OR a demographic knowledge (e.g. **census size, Nc**), and a “rule of thumb” to convert Nc to Ne, i.e. **Ne/Nc ratio**, which in many cases is close to 0.1 (Frankham 1995; and see Hoban et al. 2020, 2021). +The effective population size is the genetic complement of **census size**; where census size influences ecological aspects of a population, genetic factors of a population are influenced by Ne. Both random [allele](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#allele) frequency change and estimates of inbreeding are influenced by Ne. For the purposes of the genetic diversity indicators, Ne refers to contemporary effective population size which measures ongoing and near-term genetic drift. Estimating contemporary Ne does not require knowing mutation rates (which is required for estimating historic Ne), but does require genetic data OR a demographic knowledge (e.g. **census size, Nc**), and a “rule of thumb” to convert Nc to Ne, i.e. **Ne/Nc ratio**, which in many cases is close to 0.1 (Frankham 1995; and see Hoban et al. 2020, 2021). ### Ne/Nc ratio Relationship between the **census size (Nc)** and the **effective population size (Ne)**. This ratio enables the estimation of effective population size when only census size is known, or vice versa. It is a helpful metric for calculating genetic diversity indicators, where census size may be the most common estimate of population size. Where available, species specific ratios enable the best estimates of Ne from Nc. Where unavailable, ‘rule of thumb’ values can be used to estimate Ne (Frankham 1995; and see Hoban et al. 2020, 2021) @@ -98,7 +98,7 @@ A list of general, major habitats that species occur in, globally. Within each * ## Species' biology ### Population -In general, a population is a group of individual organisms that can mate with each other and have low or no connectivity with other populations. However, this definition can vary depending on the species. See [‘What is a population’](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer) under [‘Theoretical background’](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background) for detailed discussion of what a population is and how to define a population for assessments of genetic diversity indicators. +In general, a population is a group of individual organisms that can mate with each other and have low or no connectivity with other populations. However, this definition can vary depending on the species. See [‘What is a population’](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/What-is-a-population.html#what-is-a-population-a-first-simple-answer) under [‘Theoretical background’](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background) for detailed discussion of what a population is and how to define a population for assessments of genetic diversity indicators. ### Metapopulations A metapopulation consists of numerous groups of individuals (subpopulations), occupying multiple localities (e.g. ponds, prairies, forests etc.), that are separate but within the species’ dispersal capacity. Subpopulations within a metapopulation are thus capable of exchanging at least one migrant (one reproductive adult moving between patches) on average per generation per year. Metapopulations should represent stable spatial and temporal units. In the case of a metapopulation, the population size should be considered the sum of the individual subpopulations. @@ -120,5 +120,5 @@ are populations that went extinct in a location and have since been reintroduced - #### Reinforced populations populations are naturally occurring populations that have a native gene pool but have had new individuals introduced to support the population. Depending on the origin of the new individuals, e.g. from a breeding population or other population, the reinforced population may contain non-local genetic material. The genetic composition of such populations is therefore likely to be mostly the original gene pool of the location, though can have a combination of native gene pool and variation from other populations. -[Previous: Calculations and reporting](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting){: .btn .btn-blue .mr-4 } -[Next: Reference and other resources](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/Video_resources/References_and-resources.html#references-and-other-resources){: .btn .btn-green } +[Previous: Calculations and reporting](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/6_Calculations_and_reporting/Calculations_and_reporting.html#calculations-and-reporting){: .btn .btn-blue .mr-4 } +[Next: Reference and other resources](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/Video_resources/References_and-resources.html#references-and-other-resources){: .btn .btn-green } diff --git a/docs/Contact_cite/Contact_cite.md b/docs/Contact_cite/Contact_cite.md index b2de987..6c2db8d 100644 --- a/docs/Contact_cite/Contact_cite.md +++ b/docs/Contact_cite/Contact_cite.md @@ -21,6 +21,6 @@ If you use any of the materials of these guidelines, please cite: * Mastretta-Yanes\*, A., da Silva\*, J., Grueber, C. E., ... Laikre, L. & Hoban, S. (under review). **Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Monitoring framework**. *EcoEvoRxiv* (Pre-Print). https://ecoevorxiv.org/repository/view/6104/. DOI: [https://doi.org/10.32942/X2WK6T](https://doi.org/10.32942/X2WK6T) -[Previous: References and other resources](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/Video_resources/References_and-resources.html#references-and-other-resources){: .btn .btn-blue } +[Previous: References and other resources](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/Video_resources/References_and-resources.html#references-and-other-resources){: .btn .btn-blue } diff --git a/docs/Video_resources/References_and-resources.md b/docs/Video_resources/References_and-resources.md index a9b4a78..fe76b35 100644 --- a/docs/Video_resources/References_and-resources.md +++ b/docs/Video_resources/References_and-resources.md @@ -37,5 +37,5 @@ A short note which highlights some of the challenges to using genetic diversity For additional resources please refer to the [Coalition for Conservation Genetics Capacity Building Resource Page](https://www.coalitionforconservationgenetics.org/resources-database/category/Capacity%20building) to gain access to Policy briefs, the latest headline indicator metadata, webinars and other Capacity Building Resources and additional scientific publications. -[Previous: Glossary](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary){: .btn .btn-blue .mr-4 } -[Next: Contact & How to cite](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/Contact_cite/Contact_cite.html#get-in-touch-and-more-help){: .btn .btn-green } +[Previous: Glossary](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#glossary){: .btn .btn-blue .mr-4 } +[Next: Contact & How to cite](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/Contact_cite/Contact_cite.html#get-in-touch-and-more-help){: .btn .btn-green } diff --git a/index.md b/index.md index fed7568..696f121 100644 --- a/index.md +++ b/index.md @@ -7,7 +7,7 @@ nav_order: 1 # Guideline materials and documentation for the Genetic Diversity Indicators {: .highlight } -This guide is intended to assist nations in quantifying genetic indicator values at every stage of the process: from species selection to data compilation to indicator calculation. These materials are based on the co-creation experience of the [first multinational assessment of the genetic diversity indicators](ttps://ecoevorxiv.org/repository/view/6104/), and we hope to keep updating them as more teams share their experience. If you would like to provide feedback or have questions please [get in touch](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/Contact_cite/Contact_cite.html). +This guide is intended to assist nations in quantifying genetic indicator values at every stage of the process: from species selection to data compilation to indicator calculation. These materials are based on the co-creation experience of the [first multinational assessment of the genetic diversity indicators](ttps://ecoevorxiv.org/repository/view/6104/), and we hope to keep updating them as more teams share their experience. If you would like to provide feedback or have questions please [get in touch](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/Contact_cite/Contact_cite.html). Genetic diversity is the foundation of all biological diversity. It is **necessary for species’ populations to remain healthy and adapt to environmental change**, such as climate change, pollution, changing habitats, pests and disease. Genetic diversity is **also vital for resilience of all ecosystems** (i.e., recovery from heat waves and ocean pollution or acidification) and for the success of ecosystem restoration and the reintroduction of populations and species. Populations with low genetic diversity suffer inbreeding, low viability, and low resilience. Unfortunately, genetic diversity has declined due to habitat loss, fragmentation, overharvest, and other human activities. Yet despite all of this, genetic variation has been often neglected by many global conservation initiatives, partly due to the lack of simple and widely-applicable genetic diversity indicators. @@ -19,25 +19,25 @@ The three new genetic diversity indicators were conceived using SMART (specific, The three genetic indicators are: -* **[Effective population size (Ne) 500 indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html):** the proportion of populations within species with an effective population size (Ne) greater than 500. +* **[Effective population size (Ne) 500 indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Ne-500.html):** the proportion of populations within species with an effective population size (Ne) greater than 500. -* **[Populations Maintained (PM) indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html):** the proportion of maintained populations within species. +* **[Populations Maintained (PM) indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/PM-indicator.html):** the proportion of maintained populations within species. -* **[DNA-based monitoring indicator](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html):** number of species in which genetic diversity has been or is being monitored using DNA-based methods +* **[DNA-based monitoring indicator](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/DNA-based-monitoring-indicator.html):** number of species in which genetic diversity has been or is being monitored using DNA-based methods Thus, the genetic diversity indicators adopted at COP15 by the Global Biodiversity Framework are based on these processes to monitor what affects genetic diversity. ![](docs/PMNe500_diagram.png) -The Ne 500 indicator measures **the proportion of populations within a species that are of sufficient size to maintain genetic diversity and adaptive potential** within that species. When a population is below a certain size threshold (i.e., Ne 500), genetic diversity loss starts to occur, and at population sizes much smaller than this threshold, genetic diversity loss can be very rapid (Frankham 2021). So it is important to maintain or restore populations above this Ne 500 threshold. The ideal state for this indicator is a value of 1, indicating that all populations are of sufficient size (that each population is above Ne 500). For many species, it is sufficient and appropriate to use census size (Nc: the number of living adults) as a proxy for Ne, with the default threshold translating to Nc = 5000 mature individuals (though see Section [How to estimate population sizes](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes). **The Ne 500 indicator is likely the best evidence of genetic status and risk of genetic erosion when DNA sequencing is not available (the case for most species globally)**. +The Ne 500 indicator measures **the proportion of populations within a species that are of sufficient size to maintain genetic diversity and adaptive potential** within that species. When a population is below a certain size threshold (i.e., Ne 500), genetic diversity loss starts to occur, and at population sizes much smaller than this threshold, genetic diversity loss can be very rapid (Frankham 2021). So it is important to maintain or restore populations above this Ne 500 threshold. The ideal state for this indicator is a value of 1, indicating that all populations are of sufficient size (that each population is above Ne 500). For many species, it is sufficient and appropriate to use census size (Nc: the number of living adults) as a proxy for Ne, with the default threshold translating to Nc = 5000 mature individuals (though see Section [How to estimate population sizes](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/Populations_sizes.html#how-to-estimate-population-sizes). **The Ne 500 indicator is likely the best evidence of genetic status and risk of genetic erosion when DNA sequencing is not available (the case for most species globally)**. The PM indicator measures **the proportion of populations that still exist compared to the total number of populations that used to occur** (i.e., it is a way of quantifying population extinctions). Each population is presumed to be genetically distinct and locally adapted, and hence loss of any population within a species equates to the loss of genetic diversity and a species’ unique genetic adaptations. Similar to the Ne 500 indicator, the ideal state for this indicator is a value of 1, indicating that no populations have been lost. The DNA-based monitoring indicator **tracks the number of species being monitored temporally using DNA-based methods**. Unlike the other two indicators, the genetic monitoring indicator does not estimate the genetic health of a species directly. Instead, it is a proxy for knowledge that could support management of genetic diversity. It is a simple count of genetic studies that can relate to genetic monitoring efforts being undertaken in a country and/or relate to informing management of genetic diversity. -Over time, all of these indicators can be used to monitor progress in the overall genetic health of the biodiversity in a country, as well as species-specific recovery and general genetic management efforts. For a more in-depth look at the scientific underpinning of these indicators, see [Background](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html). +Over time, all of these indicators can be used to monitor progress in the overall genetic health of the biodiversity in a country, as well as species-specific recovery and general genetic management efforts. For a more in-depth look at the scientific underpinning of these indicators, see [Background](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html). The next Figure illustrates how these indicators can be calculated for a species of fish. @@ -83,4 +83,4 @@ If you use any of the materials listed below, please cite: * Mastretta-Yanes\*, A., da Silva\*, J., Grueber, C. E., ... Laikre, L. & Hoban, S. (under review). **Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Monitoring framework**. *EcoEvoRxiv* (Pre-Print). https://ecoevorxiv.org/repository/view/6104/. DOI: [https://doi.org/10.32942/X2WK6T](https://doi.org/10.32942/X2WK6T) -[Next: Background](https://aliciamstt.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background){: .btn .btn-green } +[Next: Background](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/2_Theoretical_background/Theoretical-background.html#background){: .btn .btn-green }