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index.md

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 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).
 
 
-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. 
+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. 
 
 Following the U.N. Convention on Biological Diversity (CBD)’s Strategic Plan for Biodiversity 2011-2020, a critical gap in global biodiversity reporting was clear - knowledge on the status and trends of genetic diversity for most species. Starting in 2020, during the preparation of what would become the Kunming Montreal Global Biodiversity Framework three genetic diversity indicators were developed. These are the first indicators that can quantitatively estimate genetic status for all species, using existing data, in a rapid manner. 
 
-The three new genetic diversity indicators were conceived using SMART (specific, measurable, achievable, realistic, and timely) criteria and can be quantified without using genetic data (e.g. without DNA sequences) - a key innovation enabling them to be applied across a wide range of taxa by countries with varying levels of resource capacities. 
+The three new genetic diversity indicators were conceived using SMART (specific, measurable, achievable, realistic, and timely) criteria and can be quantified *without using genetic data (e.g. without DNA sequences*) - a key innovation enabling them to be applied across a wide range of taxa by countries with varying levels of resource capacities. 
 
 
 The three genetic indicators are:
@@ -30,19 +30,19 @@ 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 we want 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 threshold translating to Nc = 5000 mature individuals.
+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 XX regarding this transformation and other thresholds). **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 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. Instead, it is a proxy for knowledge that could support management of genetic diversity. It is a simple count of genetic studies that can be used to track the genetic monitoring efforts being undertaken in a country to help inform adaptive species management and possibly conservation policy. 
+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).
 
 
-The next Figure illustrates how these indicators can be calculated for a species of tree.
+The next Figure illustrates how these indicators can be calculated for a species of fish.
 
-![](Fig1.png)
+![](New_Fish_Fig.png)
 
 The following video offers a short explanation of the genetic diversity indicators and the results of the first multinational assessment:
 
@@ -60,7 +60,7 @@ The Ne 500 indicator is directly relevant to **Goal A**, as it informs the healt
 
 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.
 
-As noted by [Hoban et al (2023a)](https://doi.org/10.1007/s10592-022-01492-0), the Ne 500 indicator is relevant to other targets such as sustainable harvest Targets 5 and 9 because harvested populations should be maintained at or above Ne 500. To ensure all genetically distinct populations are represented at sufficient sizes to maintain their persistence, it is relevant for DNA-based-monitoring-indicator on biodiversity inclusive spatial planning and representative protected areas, respectively, and DNA-based-monitoring-indicator for increasing area and connectivity of green and blue spaces in urban environments to promote gene flow and species recovery. 
+Genetic diversity is vital for meeting several targets (Hoban et al. 2023, 2020; Hoban, Campbell, et al. 2021; Bolam et al. 2023) such as **target 2** (effective restoration), **target 3** (30% area in effectively governed PAs and OECMs), **target 4** (management actions for recovering species and conserving genetic diversity), **target 6** (reducing invasive species), **target 8** (minimize climate impacts), **target 9** (sustainable use of wild species), **target 10** (sustainable fisheries, forestry, agriculture), **target 11** (restoring and sustaining ecosystem services), and **target 13** (equitable sharing of genetic resources).
 
 The utility of these indicators is not confined to CBD reporting and Parties to its conventions. All countries are encouraged to start quantifying these indicators to better understand the genetic status of their biodiversity to better inform biodiversity management and track species recovery.