Merge branch 'main' of https://github.com/CCGenetics/guidelines-genet…

…ic-diversity-indicators

forgot to pull after minor changes online

docs/3_Howto_guides_examples/uncertainty.md

@@ -15,7 +15,7 @@ Some documents may delineate populations in a hierarchical fashion, for example,
 ###### **Two scales of population delineation for the frecklebelly madtom (Noturus munitus) in the southeastern United States.** Watersheds (HUC10, gray outlines) were grouped into “Resilience Units” (one scale of population grouping, shown in different colors) based on barriers to dispersal, such as dams. These units were then aggregated into six larger “Representation Units” (bold numbers) delineating potential adaptive differences based on genetic, morphological, behavioral, and hydrologic variation (USFWS,2020). The populations maintained indicator varied at these two scales, with 12/16 populations maintained at the Resiliency Unit scale (PM = 0.75) vs. 5/6 populations maintained at the Representation Unit scale (PM = 0.83).
 
 
-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.
+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, or if different studies report Ne based on different genetic markers or statistical methods. See for example the [expert disagreement on the number of populations Howling monkeys](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#expert-disagreement-on-the-number-of-populations-or-nc). In that case, alternative assessments can be done, for instance with different numbers of populations.
 
 [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 }
+[Next: Example assessments](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/4b_Example_assessments/Example_assessments.html#example-assessments){: .btn .btn-green }

docs/5_Data_collection/Recommended_data.md

@@ -64,7 +64,7 @@ table th:nth-of-type(5) {
 |---|---|---|---|---|
 | **Assessment** |  |  |  |  |
 |  | Name of assessor | Character text | Alicia Mastretta-Yanes | name_assessor |
-|  | Whether the assessment of the species was done a single time (single_assessment) or more than once (multiassessment). See XXX section. | Categorical | single_assessment | multiassessment |
+|  | Whether the assessment of the species was done a single time (single_assessment) or more than once (multiassessment). See [How to account for uncertainty](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/3_Howto_guides_examples/uncertainty.html) section. | Categorical | single_assessment | multiassessment |
 | **Taxon** |  |  |  |  |
 |  | Taxonomic Authority and year for the species (or subspecies/variety) being assessed. | Character text | (Martinez, 1946) | scientific_authority |
 |  | Taxonomic Group according to a desired classification useful for summaries. *  | Categorical | mammal | taxonomic_group |
@@ -98,7 +98,7 @@ table th:nth-of-type(5) {
 |  | Realm or realms which the species inhabits | Categorical | Freshwater terrestrial | realm |
 |  | Habitat of the species according to the IUCN Habitat Classification Scheme. https://www.iucnredlist.org/resources/habitat-classification-scheme. Select all that apply. | Categorical | shrubland wetland | IUCN_habitat |
 |  | Whether the species is a national endemic | Categorical | Yes | national_endemic |
-|  | Whether the species range is wide-ranging  or restricted, based on criteria outlined in Section XXX.  | Categorical | wide_ranging | species_range |
+|  | Whether the species range is wide-ranging  or restricted, based on criteria outlined in [Glossary](https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/docs/7_Glossary/Glossary.html#species-range).  | Categorical | wide_ranging | species_range |
 |  | Global Red List Category (IUCN) | Categorical | LC | global_IUCN |
 |  | National or regional Red List Category (any red listing different to the Global) | Categorical | NT | regional_redlist |
 

index.md

@@ -7,7 +7,7 @@ nav_order: 1
 # Guideline materials and documentation for the Genetic Diversity Indicators of the monitoring framework for the Kunming-Montreal Global Biodiversity Framework
 
 {: .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](https://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).
+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 pilot multinational assessment of the genetic diversity indicators](https://ecoevorxiv.org/repository/view/6104/). The materials will be regularly kept updated through a versioning system 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. 
@@ -30,7 +30,7 @@ Thus, the genetic diversity indicators adopted at COP15 by the Global Biodiversi
 
 ![](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://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 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.
 
@@ -56,6 +56,7 @@ In December 2022, 196 Parties to the CBD adopted the Kunming-Montreal Global Bio
 ###### Components of Goal A and Target 4 of the Global Biodiversity Framework that specifically address genetic diversity.
 
 
+
 The Ne 500 indicator is directly relevant to **Goal A**, as it informs the health and resilience of species’ populations, their genetic diversity, and the threat of species extinction. Knowledge of species population’s effective size is relevant to **Target 4** as it facilitates active management of species, ex situ breeding programs and informs the conservation efforts and recovery process of species populations following environmental disruption. The Ne 500 indicator is a Headline indicator for Goal A and Target 4.
 
 The complementary indicator for Goal A, the “proportion of populations maintained”, is necessary for maintaining genetic diversity among populations. This indicator is directly relevant to addressing the “between populations” portion of **Target 4**, despite the GBF not making a direct link. Both the Ne 500 and PM indicators complement each other, and **experts agree that both are critical for assessing and monitoring the genetic health of species** (Hoban et al 2020, Hoban et al 2023b). Helpfully, quantifying the PM indicator (understanding the number of populations within a species - both extant and extinct) can be performed simultaneously to quantifying the Ne 500 indicator.
@@ -74,11 +75,9 @@ The following video offers a short explanation of the genetic diversity indicato
 
 This documentation is dual-licensed under CC BY 4.0. Attribution 4.0 Internationa for the media and all non-software materials and MIT License for the scripts and other provided code [LICENSE](https://raw.githubusercontent.com/CCGenetics/guidelines-genetic-diversity-indicators/main/LICENSE). The repository uses the [Just the Docs](https://just-the-docs.com/) theme.  
 
-The documentation was developed by the genetic diversity indicator team. 
-
 If you use any of the materials of these guidelines **please cite**:
 
-Mastretta-Yanes, A., Sofía Suárez, Rebecca Jordan, Sean Hoban, Jessica M. da Silva, Luis Castillo-Reina, Myriam Heuertz, Fumiko Ishihama, Viktoria Köppä, Linda Laikre, Joachim Mergeay, Ivan Paz-Vinas, Gernot Segelbacher, Alicia Knapps, Henry Rakoczy, Amelie Weiler & Brenna R. Forester. Guideline materials and documentation for the Genetic Diversity Indicators. https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/
+Mastretta-Yanes, A., Sofía Suárez, Rebecca Jordan, Sean Hoban, Jessica M. da Silva, Luis Castillo-Reina, Myriam Heuertz, Fumiko Ishihama, Viktoria Köppä, Linda Laikre, Joachim Mergeay, Ivan Paz-Vinas, Gernot Segelbacher, Alicia Knapps, Henry Rakoczy, Amelie Weiler & Brenna R. Forester. Guideline materials and documentation for the Genetic Diversity Indicators of the monitoring framework for the Kunming-Montreal Global Biodiversity Framework. https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/
 
 ## Acknowledgments