change aliciamstt to ccgenetics in all links

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

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
 
 
 
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docs/2_Theoretical_background/Gen_div_advantages.md

@@ -35,5 +35,5 @@ Genetic diversity indicators have multiple practical uses beyond reporting. They
 
 
 
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+[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 }

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)).
 
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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.
 
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+[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 }
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docs/2_Theoretical_background/PM-indicator.md

@@ -7,20 +7,20 @@ 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)
 ###### **Genetic diversity between populations and the Proportion of Maintained Populations indicator**. Left: Colour patterns of strawberry poison frog (Oophaga pumilio) in Nicaraguan populations ([Galindo-Uribe et al., 2014](https://www.salamandra-journal.com/index.php/contents/2014-vol-50/380-galindo-uribe-d-j-sunyer-j-s-hauswaldt-a-amezquita-h-proehl-m-vences/file)). Right: each fish population is genetically distinct and exhibits different genetic diversity (represented by the different colors). A loss of a population can therefore compromise the species’ ability to adapt to future changes. PM indicator value: 3/4 = 0.75.
 
 .
 
-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.
 
 
 
 
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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
 
 
 
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