Geology topics

Ivan Paz-Vinas

Publications and source records attributed to Ivan Paz-Vinas.

16 recordsLinked to original sources

USGS2025

Sparse genetic data limit biodiversity assessments in protected areas globally

Global conservation targets include protecting genetic diversity within species. Yet few studies have assessed whether protected areas (PAs) include genetically diverse populations across species globally. A first step is understanding the availability of population genetic data that could be used in these assessments. We surveyed georeferenced population-level nuclear (as opposed to mitochondrial or plastid-based) genetic data across continents and marine biomes (36,354 populations, 2809 species) and found substantial geographic and taxonomic gaps. Most data were concentrated in Europe and North America, with major gaps in Africa and Asia. For most taxonomic groups, data were available for <1% of described species. Globally, 52.08% of the total areal extent of PAs lacked genetically sampled populations. These gaps in data availability highlight the need for targeted genetic data collection, harmonization, and sharing to improve genetic diversity monitoring and conservation planning. Combined with proxy-based genetic indicators, such data are needed to inform PA assessments, bolster area-based conservation initiatives like 30 × 30, and support achievement of global genetic conservation targets.

Frontiers in Ecology and the Environment↗

USGS2025

A survey of mammal and fish genetic diversity across the global protected area network

Global conservation targets aim to expand protected areas and maintain species’ genetic diversity. Whether protected areas capture genetic diversity is unclear. We examined this question using a global sample of nuclear population-level microsatellite data comprising genotypes from 2513 sites, 134,183 individuals, and 176 mammal and marine fish species. The genetic diversity and differentiation of samples inside and outside protected areas were similar, with some evidence for higher diversity in protected areas for small-bodied mammals. Mammal populations, particularly large species, tended to be more genetically diverse when near multiple protected areas, regardless of whether samples were collected in or outside protected areas. Older marine protected areas tended to capture more genetically diverse fish populations. However, limited data availability in many regions hinders the systematic incorporation of genetic diversity into protected area design. Focusing on minimizing population decline and maintaining connectivity between protected areas remain essential proxies for maintaining genetic diversity.

Conservation Letters↗

USGS2024

DNA-based studies and genetic diversity indicator assessments are complementary approaches to conserving evolutionary potential

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic studies, when available, provide detailed information that is important for management, such as estimates of gene flow, inbreeding, genetic erosion and adaptation. In this article, we argue that the development and advancement of genetic diversity indicators is a complementary approach to genetic studies in conservation biology, but not a substitute. Genetic diversity indicators and empirical genetic data can provide different information for conserving genetic diversity. Genetic diversity indicators enable affordable tracking, reporting, prioritization and communication, although, being proxies, do not provide comprehensive evaluation of the genetic status of a species. Conversely, genetic methods offer detailed analysis of the genetic status of a given species or population, although they remain challenging to implement for most species globally, given current capacity and resourcing. We conclude that indicators and genetic studies are both important for genetic conservation actions and recommend they be used in combination for conserving and monitoring genetic diversity.

Conservation Genetics↗

USGS2024

Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework

Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of the taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.

Ecology Letters↗

USGS2024

Best practices for genetic and genomic data archiving

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.

Nature, Ecology and Evolution↗

USGS2024

Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity

Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size ( N e < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

BioScience↗

USGS2023

Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries

Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost-effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity.

Conservation Letters↗

USGS2023

Genetic diversity and IUCN Red List status

The International Union for Conservation of Nature (IUCN) Red List is an important and widely used tool for conservation assessment. The IUCN uses information about a species’ range, population size, habitat quality and fragmentation levels, and trends in abundance to assess extinction risk. Genetic diversity is not considered, although it affects extinction risk. Declining populations are more strongly affected by genetic drift and higher rates of inbreeding, which can reduce the efficiency of selection, lead to fitness declines, and hinder species’ capacities to adapt to environmental change. Given the importance of conserving genetic diversity, attempts have been made to find relationships between red-list status and genetic diversity. Yet, there is still no consensus on whether genetic diversity is captured by the current IUCN Red List categories in a way that is informative for conservation. To assess the predictive power of correlations between genetic diversity and IUCN Red List status in vertebrates, we synthesized previous work and reanalyzed data sets based on 3 types of genetic data: mitochondrial DNA, microsatellites, and whole genomes. Consistent with previous work, species with higher extinction risk status tended to have lower genetic diversity for all marker types, but these relationships were weak and varied across taxa. Regardless of marker type, genetic diversity did not accurately identify threatened species for any taxonomic group. Our results indicate that red-list status is not a useful metric for informing species-specific decisions about the protection of genetic diversity and that genetic data cannot be used to identify threat status in the absence of demographic data. Thus, there is a need to develop and assess metrics specifically designed to assess genetic diversity and inform conservation policy, including policies recently adopted by the UN's Convention on Biological Diversity Kunming-Montreal Global Biodiversity Framework.

Conservation Biology↗

USGS2023

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Conservation Genetics↗

USGS2022

Global genetic diversity status and trends: Towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within-species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: ( i ) Genetic Diversity; ( ii ) Genetic Differentiation; ( iii ) Inbreeding; and ( iv ) Effective Population Size ( N e ). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large-scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long-term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Biological Reviews↗

USGS2021

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics↗

USGS2021

Authors’ reply to letter to the editor: Continued improvement to genetic diversity indicator for CBD

We appreciate the encouraging response to our call for indicators for genetic diversity within the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity, CBD (Laikre et al. 2020 ; Hoban et al. 2020 ). In agreement with us, Frankham ( 2021 ) highlights the urgent necessity for the CBD to include an indicator that tracks the maintenance of genetic diversity within populations of all species—wild and domestic. Draft CBD Headline indicators (which all CBD Parties will need to report) do not include genetic diversity within populations of wild species (CBD/SBSTTA/24/3Add.1).

Conservation Genetics↗

USGS2021

Macrogenetic studies must not ignore limitations of genetic markers and scale

Millette et al . (Ecology Letters, 2020, 23:55–67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

Ecology Letters↗

USGS2021

Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees

Fady & Bozzano highlight some challenges to a proposed Convention on Biological Diversity (CBD) indicator of genetic diversity based on effective population size, Ne ( Fady and Bozzano, 2020 ; Hoban et al., 2020 ). We appreciate the thoughtful debate and concur that genetic diversity indicators must be reliable and scalable. We fully agree that “genetic diversity should be better considered in the CBD post-2020 framework to prevent the irreplaceable loss of biodiversity… existing indicators are far from satisfactory.” As Fady & Bozzano state, Ne is essential for monitoring vital aspects of genetic diversity: loss of genetic diversity due to drift (genetic erosion), inbreeding rate (genetic health), and potential for adaptation and long term survival (resilience) ( Fady and Bozzano, 2020 ).

Biological Conservation↗

USGS2020

Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics . Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.

Biological Conservation↗

USGS2020

Proposed species extinction target fails to capture the diversity in biodiversity

We believe the 20 species extinction metric is a retrograde proposal, which does not adequately consider the lessons learnt from the 2020 Aichi Biodiversity Targets. Whilst having a single simple overarching target is appealing, we believe a positively-framed target will garner support, rather than one that aims to, at best, limit negative impacts. The Convention on Biological Diversity’s zero draft states that future targets should be clear, consistent and SMART (Specific, Measurable, Achievable, Relevant and Timely). Extinction is problematic as a standalone target: it can take decades to demonstrate and therefore cannot be measured over a relevant time-period, and is biased towards terrestrial vertebrates. The proposal is not scalable across nations, nor is it equitable,one of the key aspirations of the zero draft. Many industrialised countries are unlikely to find the targets challenging because their most vulnerable species have largely gone extinct; tropical species-rich countries, where much biodiversity is yet to be catalogued, will find the targets demanding and unachievable in the short- or medium-term. Despite the authors’ statement to the contrary, species extinction is not necessarily relevant to other aspects of biodiversity, such as ecosystems or genetic diversity. A species may be reduced to a small fraction of its former extent without going extinct. However, its ecosystem will be altered, and its contribution to ecosystem functions and the socio-economic benefits it provided will be lost. The focus on extinction is not novel and has not been particularly successful to date, as demonstrated by the decline of emblematic species such as rhinoceroses. Alternatively, composite indicators can be used to capture biodiversity’s three fundamental components (ecosystems, species and genetic diversity). In conclusion, we cannot support a target that fails to represent the diversity in biodiversity and, in the authors’ words, could be met despite “wholesale and damaging changes to life on Earth.”

Science↗