Developing a monitoring program of genetic diversity: what do stakeholders say?

AbstractGenetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and species. National and international legislation increasingly mandates a monitoring of genetic diversity. Examples are the United Nation’s Convention on Biological Diversity (CBD) Aichi target 13 and the current post-2020 negotiations to specify a new target for maintaining genetic diversity. To date, only a few pilot projects have been launched that systematically monitor genetic diversity over time in natural populations of a broad variety of wild species. The Swiss Federal Office for the Environment mandated a feasibility study in 2019 for implementing a national monitoring of genetic diversity in natural populations. To obtain information on whether stakeholders are interested in such a systematic monitoring, what they would expect from such a monitoring and where they see respective caveats, we conducted an online survey, which 138 (42% of those surveyed) Swiss stakeholders answered. We find that Swiss stakeholders are generally aware of the lacking evidence regarding the status of genetic diversity in wild populations and species. Accordingly, most stakeholders are interested in a monitoring of genetic diversity and see opportunities for the application of its results in their work. Nevertheless, stakeholders also expressed concerns regarding financial resources and that the results of a genetic diversity monitoring program would not benefit conservation practice. Our findings highlight the importance of stakeholder engagement and demonstrate the value of a detailed stakeholder analysis prior to developing and implementing a genetic diversity monitoring program. A powerful tool for examining the constellation and interactions of the different stakeholders are social network analyses (SNAs). Finally, it is particularly important to communicate transparently about the possibilities and limitations of a genetic diversity monitoring program as well as to closely involve stakeholders from the beginning to increase the acceptance of genetic diversity monitoring and facilitate its implementation.

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Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

10.22541/au.163900315.52745564/v1 ◽

2021 ◽

Author(s):

Anastasia Andersson ◽

Sten Karlsson ◽

Nils Ryman ◽

Linda Laikre

Keyword(s):

Genetic Diversity ◽

Brown Trout ◽

Biological Diversity ◽

Molecular Genetic ◽

Convention On Biological Diversity ◽

Effective Population ◽

Sympatric Populations ◽

Term Survival ◽

Molecular Genetic Data ◽

Science Management

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. To test newly proposed indicators, we monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout inhabiting 27 small mountain lakes representing 10 water systems in central Sweden. Three of the indicators were previously proposed for broad, international use for the Convention on Biological Diversity (CBD) context, while three others were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations and assess the effective population size (Ne). We used a panel of 96 SNPs and identified 29 discrete populations retained over time. Over 40 percent of the lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Although statistically significant genetic diversity reductions occurred in several populations, they were mostly within proposed threshold limits. Metapopulation structure appears to buffer against diversity loss; when applying the indicators to metapopulations most indicators suggest an acceptable genetic status in all but one system. The CBD indicators agreed with the national ones but provided less detail. We propose that all indicators applied here are appropriate for monitoring genetic diversity within species.

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Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽

10.3390/biotech10040023 ◽

2021 ◽

Vol 10 (4) ◽

pp. 23

Author(s):

Oxana Khapilina ◽

Ainur Turzhanova ◽

Alevtina Danilova ◽

Asem Tumenbayeva ◽

Vladislav Shevtsov ◽

...

Keyword(s):

Genetic Diversity ◽

Endemic Species ◽

Biological Diversity ◽

Natural Populations ◽

Subsequent Development ◽

Dna Profiling ◽

Primer Binding Site ◽

Anthropogenic Factors ◽

Habitat Specificity ◽

Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

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Research Concerning Cucumber (Cucumis Sativus L. Mill) Genetic Diversity

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Agriculture ◽

10.15835/buasvmcn-agr:6531 ◽

2011 ◽

Vol 68 (2) ◽

Author(s):

Aurel MAXIM ◽

Mignon ŞANDOR ◽

Lucia MIHALESCU ◽

Ovidiu MAXIM ◽

Oana MARE ROŞCA

Keyword(s):

Genetic Diversity ◽

Biological Diversity ◽

Genetic Erosion ◽

Farming Systems ◽

Convention On Biological Diversity ◽

Cultivated Plants ◽

Cucumis Sativus L ◽

Local Varieties ◽

Industrial Farming ◽

The University

During the second part of the twentieth century the cultivated plants have been faced with genetic erosion, because of the expandinding industrial farming systems. The sustainable agriculture can not exist without a rich genetic diversity. After the United Nations Conference from Rio de Janeiro (1992), when the Convention on Biological Diversity was adopted, a series of acts and european references that protect agrobiodiversity had emerged. Between 2007 and 2010, at the University of Agricultural Sciences and Veterinary Medicine a program which aims to identify and conserve local vegetable varieties was conducted. Out of 290 cultivars, 171 (58.9%) were genuine local varieties. There were collected 12 cucumber cultivars from the following counties: Salaj (7), Cluj (3), Bistrita-Nasaud (1) and Satu-Mare (1). The morphologic caractheristics proved that all this 12 cultivars were authentic and valuable local varieties. The local varieties were agronomical, biological and biochemical characterized, both in field and laboratory. The seeds achieved from those 12 local varieties were preserved in the Suceava Gene Bank, from where stakeholders (farmers, agronomists, researchers) can obtain seeds.

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Biodiversity Along Core–Periphery Clines

Biodiversity in Drylands ◽

10.1093/oso/9780195139853.003.0008 ◽

2005 ◽

Author(s):

Sergei Volis ◽

Salit Kark

Keyword(s):

Genetic Diversity ◽

Species Diversity ◽

Biological Diversity ◽

Morphological Diversity ◽

Spatial Location ◽

Convention On Biological Diversity ◽

Conservation Priorities ◽

Past Century ◽

Geographical Patterns ◽

Local Populations

The study of biodiversity has received wide attention in recent decades. Biodiversity has been defined in various ways (Gaston and Spicer, 1998, Purvis and Hector 2000, and chapters in this volume). Discussion regarding its definitions is dynamic, with shifts between the more traditional emphasis on community structure to emphasis on the higher ecosystem level or the lower population levels (e.g., chapters in this volume, Poiani et al. 2000). One of the definitions, proposed in the United Nations Convention on Biological Diversity held in Rio de Janeiro (1992) is “the diversity within species, between species and of ecosystems.” The within-species component of diversity is further defined as “the frequency and diversity of different genes and/or genomes . . .” (IUCN 1993) as estimated by the genetic and morphological diversity within species. While research and conservation efforts in the past century have focused mainly on the community level, they have recently been extended to include the within-species (Hanski 1989) and the ecosystem levels. The component comprising within-species genetic and morphological diversity is increasingly emphasized as an important element of biodiversity (UN Convention 1992). Recent studies suggest that patterns of genetic diversity significantly influence the viability and persistence of local populations (Frankham 1996, Lacy 1997, Riddle 1996, Vrijenhoek et al. 1985). Revealing geographical patterns of genetic diversity is highly relevant to conservation biology and especially to explicit decision-making procedures allowing systematic rather than opportunistic selection of populations and areas for in situ protection (Pressey et al. 1993). Therefore, studying spatial patterns in within-species diversity may be vital in defining and prioritizing conservation efforts (Brooks et al. 1992). Local populations of a species often differ in the ecological conditions experienced by their members (Brown 1984, Gaston 1990, Lawton et al. 1994). These factors potentially affect population characteristics, structure, and within-population genetic and morphological diversity (Brussard 1984, Lawton 1995, Parsons 1991). The spatial location of a population within a species range may be related to its patterns of diversity (Lesica and Allendorf 1995). Thus, detecting within-species diversity patterns across distributional ranges is important for our understanding of ecological and evolutionary (e.g., speciation) processes (Smith et al. 1997), and for the determination of conservation priorities (Kark 1999).

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DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

PeerJ ◽

10.7717/peerj.10674 ◽

2021 ◽

Vol 9 ◽

pp. e10674

Author(s):

Oxana Khapilina ◽

Olesya Raiser ◽

Alevtina Danilova ◽

Vladislav Shevtsov ◽

Ainur Turzhanova ◽

...

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Biological Diversity ◽

Vegetative Reproduction ◽

Natural Populations ◽

Mobile Genetic Elements ◽

Ice Age ◽

Conservation Strategy ◽

Relict Species ◽

Genetic Elements

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

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The Ira Moana Project: A Genetic Observatory for Aotearoa’s Marine Biodiversity

Frontiers in Marine Science ◽

10.3389/fmars.2021.740953 ◽

2021 ◽

Vol 8 ◽

Author(s):

Libby Liggins ◽

Cory Noble ◽

Keyword(s):

Genetic Diversity ◽

Biological Diversity ◽

Habitat Degradation ◽

Genetic Data ◽

Convention On Biological Diversity ◽

Marine Biodiversity ◽

Data Governance ◽

Data Resource ◽

Genetic Biodiversity ◽

Research Activities

The genetic diversity of populations plays a crucial role in ensuring species and ecosystem resilience to threats such as climate change and habitat degradation. Despite this recognized importance of genetic diversity, and its relevance to the Convention on Biological Diversity and the United Nations Sustainable Development Goals, it remains difficult to observe and synthesize genetic data at a national scale. The “Ira Moana—Genes of the Sea—Project” (https://sites.massey.ac.nz/iramoana/) has worked to improve stewardship of genetic data for Aotearoa New Zealand’s (NZ) marine organisms to facilitate marine genetic biodiversity observation, research, and conservation. The Ira Moana Project has established interoperable data infrastructures and tools that help researchers follow international best-practice (including the FAIR Principles for Data Stewardship and CARE Principles for Indigenous Data Governance) and contribute to a national genetic data resource. Where possible, the Project has employed existing infrastructures (such as the Genomic Observatories Metadatabase, GEOME) to allow interoperability with similar research activities, but has also innovated to accommodate the national interests of NZ. The Ira Moana Project has an inclusive model, and through presentations, workshops, and datathons, it has provided training, education, and opportunities for collaboration among NZ researchers. Here, we outline the motivations for the Ira Moana Project, describe the Project activities and outcomes, and plans for future development. As a timely response to national and international pressures on genetic biodiversity research, it is hoped that the Ira Moana Project will facilitate NZ researchers, communities, and conservation practitioners to navigate this crucial period, and provide tangible solutions nationally and globally.

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The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand

PLoS ONE ◽

10.1371/journal.pone.0250422 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0250422

Author(s):

Richard C. Winkworth ◽

Stanley E. Bellgard ◽

Patricia A. McLenachan ◽

Peter J. Lockhart

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

Geographic Distribution ◽

Complete Mitochondrial Genome ◽

Recent Common Ancestor ◽

Term Survival ◽

Network Analyses ◽

Most Recent Common Ancestor ◽

Alternative Hypotheses ◽

Tree Building

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0–304.4 years and 95% HPDs of 206.9–414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.

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Genetic diversity and sustainable management of animal genetic resources, globally

Animal Genetic Resources Information ◽

10.1017/s1014233900002327 ◽

2007 ◽

Vol 41 ◽

pp. 45-52 ◽

Cited By ~ 4

Author(s):

E. Fimland

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Sustainable Management ◽

Biological Diversity ◽

Convention On Biological Diversity ◽

Developmental Trend ◽

Animal Genetic Resources ◽

Global Responsibility ◽

Breeding Populations ◽

Commercial Breeding

SummaryGeneral trends of development imply an increasing uniformity of animal genetic resources, caused by the loss of endangered breeds and increased inbreeding within commercial breeding populations. The implications of these trends point to a reduction in the genetic diversity of the animal genetic resources, which may reduce possibilities for utilization in the future, while at the same time a dramatic change in environmental production conditions can be observed. In order to change this developmental trend, sustainable management of animal genetic resources must be promoted globally. The fundamental issues for such sustainable management are illustrated by the principles given in the Convention on Biological Diversity. In order to accomplish sustainable management of these resources, the following actions must be taken:• The development of policies to promote national and global responsibility for maintaining genetic diversity, which will not be addressed within this paper• The development of knowledge as a fundamental concept to impose sustainable management principles on these animal genetic resources. This will be dealt with in this paper. A more complete description of these features can be found in Woolliams et al, 2005 in (Sustainable Management of Animal Genetic Resources).

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Neglect of Genetic Diversity in Implementation of the Convention on Biological Diversity

Conservation Biology ◽

10.1111/j.1523-1739.2009.01425.x ◽

2010 ◽

Vol 24 (1) ◽

pp. 86-88 ◽

Cited By ~ 101

Author(s):

LINDA LAIKRE ◽

FRED W. ALLENDORF ◽

LAUREL C. ARONER ◽

C. SCOTT BAKER ◽

DAVID P. GREGOVICH ◽

...

Keyword(s):

Genetic Diversity ◽

Biological Diversity ◽

Convention On Biological Diversity

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Genetic diversity of fragmented natural populations of Pyrenacantha volubilis Wight. in India

10.21203/rs.3.rs-833939/v1 ◽

2021 ◽

Author(s):

Arjun Ramachandran ◽

A. V. Santhoshkumar ◽

Deepu Mathew ◽

Manju Elizabeth ◽

Jiji Joseph ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Inter Simple Sequence Repeat ◽

Morphological Data ◽

Cancer Drug ◽

Term Survival ◽

Anti Cancer ◽

Tree Algorithms ◽

Nj Tree ◽

First Time

Abstract Pyrenacantha volubilis Wight. is a dioecious liana occurring in small, clustered populations. The species had no documented use until the recent past, when it was identified to be a source of a highly traded anti-cancer drug – camptothecin. In the present study, we examine the genetic diversity of 12 fragmented natural populations of P. volubilis using morphological and molecular traits. Twelve polymorphic Inter Simple Sequence Repeat (ISSR) primers and 29 agromorphological traits were used to discriminate the populations using UPGMA and NJ tree algorithms respectively. The ISSR amplicon profile had 133 distinct bands. The maximum number of amplicons were produced by UBC 844 (20 bands) and the average polymorphism was 80.07 per cent. The dendrograms obtained based on molecular and agro-morphological data are in close congruence. The Thiruvananthapuram population stood apart in both the analyses as a discrete outgroup: perhaps a consequence of local adaptation. Substantial genetic diversity exists among populations. This could be tapped in domestication, which is the only way forward for the long-term survival of this species. We also report for the first time a standardized method for extraction of genomic DNA from the leaves of P. volubilis.

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