Declining population sizes and loss of genetic diversity in commercial fishes: a simple method for a first diagnostic

Exploited fish species may have or are experiencing declines in population sizes coupled with a decrease in genetic diversity. This can lead to the loss of adaptive potential to face current and future environmental changes. However, little is known about this subject while research on it is urgently needed. Thus, this study aims to answer a simple, even naive question, given the complexity of the subject: Could we use a simple method to obtain information on the loss of genetic diversity in exploited fish species? We investigated the use of the levels of genetic diversity in the widely used genetic marker Cytochrome C Oxidase subunit I (COI) mitochondrial gene. Estimates of genetic diversity in COI were obtained for populations of seven fish species with different commercial importance from the East China Sea. These estimates were contrasted against a large dataset of fish species distributed worldwide (N=1426), a dataset of East-Asian fish species (N=118), two farmed species with expected low genetic diversity, and four long-term managed species from the Mediterranean Sea. We found that estimates of genetic diversity in COI match the expectations from theoretical predictions, known population declines, and fishing pressures. Thus, the answer to our question is affirmative and we conclude that estimates of genetic diversity in COI provide an effective first diagnostic of the conservation status of exploited fish species. This simple and cost-effective tool can help prioritize research, management, and conservation on species with suspected loss of genetic diversity potentially eroding their adaptive potential to global change.

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Population diversity and relatedness in Sugarbirds (Promeropidae:Promeropsspp.)

PeerJ ◽

10.7717/peerj.5000 ◽

2018 ◽

Vol 6 ◽

pp. e5000

Author(s):

Evan S. Haworth ◽

Michael J. Cunningham ◽

Kathleen M. Calf Tjorve

Keyword(s):

Genetic Diversity ◽

Mitochondrial Gene ◽

Conservation Status ◽

Tail Length ◽

Population Diversity ◽

Breeding Systems ◽

Effective Population ◽

Socially Monogamous ◽

Population Sizes ◽

Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops caferandP. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data,P. gurneyiare in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity inP. caferfrom Helderberg Nature Reserve andP. gurneyifrom Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

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Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.)

10.7287/peerj.preprints.26619v1 ◽

2018 ◽

Author(s):

Evan S Haworth ◽

Michael J Cunningham ◽

Kathleen M. Calf Tjorve

Keyword(s):

Genetic Diversity ◽

Mitochondrial Gene ◽

Conservation Status ◽

Tail Length ◽

Population Diversity ◽

Breeding Systems ◽

Effective Population ◽

Socially Monogamous ◽

Population Sizes ◽

Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Cape Town and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

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Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.)

10.7287/peerj.preprints.26619 ◽

2018 ◽

Author(s):

Evan S Haworth ◽

Michael J Cunningham ◽

Kathleen M. Calf Tjorve

Keyword(s):

Genetic Diversity ◽

Mitochondrial Gene ◽

Conservation Status ◽

Tail Length ◽

Population Diversity ◽

Breeding Systems ◽

Effective Population ◽

Socially Monogamous ◽

Population Sizes ◽

Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Cape Town and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

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Inbreeding and loss of genetic diversity increase extinction risk

A Practical Guide for Genetic Management of Fragmented Animal and Plant Populations ◽

10.1093/oso/9780198783411.003.0003 ◽

2019 ◽

pp. 31-48

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Inbreeding Depression ◽

Environmental Changes ◽

Extinction Risk ◽

Raw Material ◽

Heterozygote Advantage ◽

Isolated Populations ◽

Survival And Reproduction ◽

Loss Of Genetic Diversity ◽

Harmful Effects

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

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Broad and fine-scale threats on threatened Brazilian freshwater fish: variability across hydrographic regions and taxonomic groups

Biota Neotropica ◽

10.1590/1676-0611-bn-2020-0980 ◽

2021 ◽

Vol 21 (2) ◽

Author(s):

Murilo Luiz e Castro Santana ◽

Fernando Rogério Carvalho ◽

Fabrício Barreto Teresa

Keyword(s):

Freshwater Fish ◽

Habitat Loss ◽

Fish Species ◽

Threatened Species ◽

Environmental Changes ◽

Anthropogenic Impacts ◽

Conservation Status ◽

Fine Scale ◽

Hydrographic Regions ◽

Taxonomic Groups

Abstract: Anthropogenic environmental changes are the main cause of species extinction during the Holocene. Species have been exposed to major source of threats, such as habitat loss and fragmentation, pollution, introduced species, and harvesting, many of which are derived from specific anthropogenic activities, such as urbanization, agriculture, and damming (i.e. fine-scale threats). However, the importance of these threats on the species conservation status in a given region depends on the type of impacts they are exposed to and the susceptibility of species to these impacts. In this study, we used a database of threatened Brazilian freshwater fish species to test whether the major source of threats and the specific anthropogenic impacts to species vary across hydrographic regions and taxonomic groups. Our results showed that habitat loss is a ubiquitous major threat jeopardizing the conservation status of the Brazilian fish species. However, different fine-scale threats mediate this process across hydrographic regions and taxonomic groups. The combination of impacts from agriculture, deforestation, and urbanization affects most of the threatened species in the basins of the Northeast, South, and Southeast, including the species of the most threatened order, the Cyprinodontiformes. Damming is the main human activity affecting threatened species of Siluriformes, Characiformes, Gymnotiformes, and Cichliformes, especially in northern basins (Amazon and Tocantins-Araguaia). Therefore, we found that specific fine-scale threats influencing threatened species vary across hydrographic regions and taxonomic groups, probably due to geographic variability in the incidence of human activities and differential niche requirements and vulnerability of species to these activities.

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Continent-wide effects of urbanization on bird and mammal genetic diversity

10.1101/733170 ◽

2019 ◽

Author(s):

C. Schmidt ◽

M. Domaratzki ◽

R.P. Kinnunen ◽

J. Bowman ◽

C.J. Garroway

Keyword(s):

Genetic Diversity ◽

Environmental Changes ◽

Bird Species ◽

Population Level ◽

Natural Environments ◽

Population Declines ◽

Effective Population ◽

Human Footprint ◽

Rate Of Increase ◽

Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

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Genomic signatures of recent adaptation in a wild bumblebee

10.1101/2021.05.27.445509 ◽

2021 ◽

Author(s):

Thomas Joseph Colgan ◽

Andres N Arce ◽

Richard J Gill ◽

Ana Ramos Rodrigues ◽

Abdoulie Kanteh ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Changes ◽

Bombus Terrestris ◽

Conservation Strategies ◽

Adaptive Potential ◽

Behavioral Experiments ◽

Environmental Pressures ◽

Genomic Signatures ◽

Environmental Interactions ◽

Future Challenges

Behavioral experiments and analyses of observation records have shown that environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects or other animals can adapt in response to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome. More specifically, we find that selection recently affected key processes underpinning environmental interactions, including neurobiology, wing development, and response to xenobiotics. We also discover unusual features of the genome, including a 53-gene region that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. The genetic diversity and gene flow we observe for this species could support its resilience to ongoing and future challenges. Overall, we provide important insight on the genetic health of an ecologically and economically important pollinator and reveal mechanisms by which it has recently adapted. The approach we used could help to understand how species differ in their adaptive potential, and to develop conservation strategies for those most at risk.

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Genetic diversity and conservation of the endemic tuco-tuco Ctenomys ibicuiensis (Rodentia: Ctenomyidae)

Journal of Mammalogy ◽

10.1093/jmammal/gyaa119 ◽

2020 ◽

Author(s):

Mayara Delagnelo Medeiros ◽

Daniel Galiano ◽

Bruno Busnello Kubiak ◽

Paula Angélica Roratto ◽

Thales Renato Ochotorena de Freitas

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Environmental Changes ◽

Isolation By Distance ◽

Conservation Status ◽

Significant Risk ◽

Structured Populations ◽

Small Range ◽

High Genetic Diversity ◽

Landscape Modification

Abstract Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.

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Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

10.1101/2020.09.30.319681 ◽

2020 ◽

Author(s):

Pamela Vega-Polo ◽

Maria M. Cobo ◽

Andrea Argudo ◽

Bernardo Gutierrez ◽

Jennifer Rowntree ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Environmental Changes ◽

Isolation By Distance ◽

Anthropogenic Activities ◽

Conservation Status ◽

Ecological Factors ◽

Andean Region ◽

Key Factor ◽

Distance Model

AbstractThe Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 homologous SSR markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE=0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated to the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystems as a whole.

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Molecular evolutionary consequences of island colonisation

10.1101/014811 ◽

2015 ◽

Author(s):

Jennifer James ◽

Robert Lanfear ◽

Adam Eyre-Walker

Keyword(s):

Genetic Diversity ◽

Population Bottleneck ◽

Surprising Result ◽

Population Bottlenecks ◽

Adaptive Potential ◽

Effective Population ◽

Island Species ◽

Population Sizes ◽

Evolutionary Consequences ◽

The Relationship

Island endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.

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