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Kaminski M, Brown JI, Seibert SR, Hernández F, Duya MV, Fontanilla IKC, Roshier D, Miles A, Joseph L, Peters JL, Lavretsky P. Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data. Mol Phylogenet Evol 2024; 197:108085. [PMID: 38688441 DOI: 10.1016/j.ympev.2024.108085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
AIM We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LOCATION Oceania, greater Indonesia, and the Philippines. TAXON Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. RESULTS Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. MAIN CONCLUSIONS Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.
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Affiliation(s)
- Marissa Kaminski
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Upper Midwest Environmental Sciences Center, United States Geological Survey, La Crosse, WI, USA.
| | - Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Sara R Seibert
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Melizar V Duya
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Ian Kendrich C Fontanilla
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - David Roshier
- School of Animal and Veterinary Science, University of Adelaide, Roseworthy SA, Australia
| | - Adam Miles
- Department of Marine and Wildlife Resources, Pago Pago, 96799, American Samoa
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
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Camus L, Gautier M, Boitard S. Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability? Evol Appl 2024; 17:e13709. [PMID: 38884022 PMCID: PMC11178484 DOI: 10.1111/eva.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/04/2024] [Indexed: 06/18/2024] Open
Abstract
Predicting the risk of establishment and spread of populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation to a new environment with genomic data via so-called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species but have still rarely been used in this context. Here, we evaluated the relationship between GO and the establishment probability of a population in a new environment using both in silico and empirical data. First, we designed invasion simulations to evaluate the ability to predict establishment probability of two GO computation methods (Geometric GO and Gradient Forest) under several conditions. Additionally, we aimed to evaluate the interpretability of absolute Geometric GO values, which theoretically represent the adaptive genetic distance between populations from distinct environments. Second, utilizing public empirical data from the crop pest species Bactrocera tryoni, a fruit fly native from Northern Australia, we computed GO between "source" populations and a diverse range of locations within invaded areas. This practical application of GO within the context of a biological invasion underscores its potential in providing insights and guiding recommendations for future invasion risk assessment. Overall, our results suggest that GO statistics represent good predictors of the establishment probability and may thus inform invasion risk, although the influence of several factors on prediction performance (e.g., propagule pressure or admixture) will need further investigation.
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Affiliation(s)
- Louise Camus
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Simon Boitard
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
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Jones GM, Goldberg JF, Wilcox TM, Buckley LB, Parr CL, Linck EB, Fountain ED, Schwartz MK. Fire-driven animal evolution in the Pyrocene. Trends Ecol Evol 2023; 38:1072-1084. [PMID: 37479555 DOI: 10.1016/j.tree.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023]
Abstract
Fire regimes are a major agent of evolution in terrestrial animals. Changing fire regimes and the capacity for rapid evolution in wild animal populations suggests the potential for rapid, fire-driven adaptive animal evolution in the Pyrocene. Fire drives multiple modes of evolutionary change, including stabilizing, directional, disruptive, and fluctuating selection, and can strongly influence gene flow and genetic drift. Ongoing and future research in fire-driven animal evolution will benefit from further development of generalizable hypotheses, studies conducted in highly responsive taxa, and linking fire-adapted phenotypes to their underlying genetic basis. A better understanding of evolutionary responses to fire has the potential to positively influence conservation strategies that embrace evolutionary resilience to fire in the Pyrocene.
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Affiliation(s)
- Gavin M Jones
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA.
| | - Joshua F Goldberg
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA
| | - Taylor M Wilcox
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - Lauren B Buckley
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Catherine L Parr
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L3 5TR, UK; Department of Zoology and Entomology, University of Pretoria, Pretoria 0028, South Africa; School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits 2050, South Africa
| | - Ethan B Linck
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Emily D Fountain
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, USA
| | - Michael K Schwartz
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
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Olazcuaga L, Lincke B, DeLacey S, Durkee LF, Melbourne BA, Hufbauer RA. Population demographic history and evolutionary rescue: Influence of a bottleneck event. Evol Appl 2023; 16:1483-1495. [PMID: 37622091 PMCID: PMC10445088 DOI: 10.1111/eva.13581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
Rapid environmental change presents a significant challenge to the persistence of natural populations. Rapid adaptation that increases population growth, enabling populations that declined following severe environmental change to grow and avoid extinction, is called evolutionary rescue. Numerous studies have shown that evolutionary rescue can indeed prevent extinction. Here, we extend those results by considering the demographic history of populations. To evaluate how demographic history influences evolutionary rescue, we created 80 populations of red flour beetle, Tribolium castaneum, with three classes of demographic history: diverse populations that did not experience a bottleneck, and populations that experienced either an intermediate or a strong bottleneck. We subjected these populations to a new and challenging environment for six discrete generations and tracked extinction and population size. Populations that did not experience a bottleneck in their demographic history avoided extinction entirely, while more than 20% of populations that experienced an intermediate or strong bottleneck went extinct. Similarly, among the extant populations at the end of the experiment, adaptation increased the growth rate in the novel environment the most for populations that had not experienced a bottleneck in their history. Taken together, these results highlight the importance of considering the demographic history of populations to make useful and effective conservation decisions and management strategies for populations experiencing environmental change that pushes them toward extinction.
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Affiliation(s)
- Laure Olazcuaga
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Beatrice Lincke
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Sarah DeLacey
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Lily F. Durkee
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Brett A. Melbourne
- Department of Ecology & Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Ruth A. Hufbauer
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
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The Relationship between Inbreeding and Fitness Is Different between Two Genetic Lines of European Bison. DIVERSITY 2023. [DOI: 10.3390/d15030368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The pedigree data for European bison are published in the European Bison Pedigree Book, established one hundred years ago. The species passed a serious bottleneck and was kept in captivity for more than 30 years. After reintroduction, some individuals were captured and moved to enclosures, which caused gaps in pedigree data. To prevent the underestimation of inbreeding value, only animals with a fully known pedigree were used in the analysis. European bison were divided into two genetic lines, Lowland-Caucasian (LC) and Lowland (LB), with different numbers of founders (all 12 vs. 7 of them). The relation between inbreeding and survival up to one month of age, calculated using logistic regression, gave different results for every genetic line. In the LC line (N = 5441), the average inbreeding level was equal to 0.253 and the influence into survival was negative (exp(B) = 0.190), but in the LB line (N = 1227), the inbreeding level was much higher (0.410) but the influence into survival was positive (exp(B) = 6.596). It could be assumed that the difference between lines is a result of purging in the first period of species restitution.
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Spießberger M, Burgstaller S, Mesnil M, Painter MS, Landler L. Telemetry and Accelerometer Tracking of Green Toads in an Urban Habitat: Methodological Notes and Preliminary Findings. DIVERSITY 2023; 15:328. [PMID: 36998310 PMCID: PMC7614386 DOI: 10.3390/d15030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Advancements in tracking technologies provide an increasingly important tool in animal monitoring and conservation that can describe animal spatial behavior in native habitats and uncover migratory routes that otherwise may be difficult or impossible to map. In addition, high-resolution accelerometer sensors provide powerful insights into animal activity patterns and can help to identify specific behaviors from accelerometer profiles alone. Previously, such accelerometers were restricted to larger animals due to size and mass constraints. However, recent advances make it possible to use such devices on smaller animals such as the European green toad (Bufotes viridis), the focus of our current study. We deploy custom made tracking devices, that consist of very-high-frequency transmitters and tri-axial accelerometers, to track toads in their native urban environment in Vienna (Austria). A total of nine toads were tracked, ranging from three to nine tracking days per individual during the post-breeding season period. We demonstrate that our devices could reliably monitor toad movement and activity during the observation period. Hence, we confirmed the predominantly nocturnal activity patterns and recorded low overall movement at this urban site. Accelerometer data revealed that toads exhibited brief but intense activity bursts between 10 pm and midnight, resting periods during the night and intermittent activity during the day. Positional tracking alone would have missed the major activity events as they rarely resulted in large positional displacements. This underscores the importance of and value in integrating multiple tracking sensors for studies of movement ecology. Our approach could be adapted for other amphibians or other animals with mass constraints and may become standard monitoring equipment in the near future.
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Affiliation(s)
- Magdalena Spießberger
- Institute of Zoology, University of Natural Resources and Life Sciences (BOKU), 1180 Vienna, Austria
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Stephan Burgstaller
- Institute of Zoology, University of Natural Resources and Life Sciences (BOKU), 1180 Vienna, Austria
| | - Marion Mesnil
- UniLaSalle, Polytechnical Institute, Campus of Beauvais, 19 Rue Pierre Waguet, 60000 Beauvais, France
| | - Michael S. Painter
- Department of Biology, Barry University, 11300 NE 2nd Ave, Miami, FL 33161, USA
| | - Lukas Landler
- Institute of Zoology, University of Natural Resources and Life Sciences (BOKU), 1180 Vienna, Austria
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Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire. Sci Rep 2023; 13:480. [PMID: 36627361 PMCID: PMC9831986 DOI: 10.1038/s41598-023-27587-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.
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Haye PA, Segovia NI, Vera R, Acuña E. Phylogeography reveals a panmictic population of the Chilean nylon shrimp along its exploitation range in the southeast Pacific Ocean. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Meiring C, Schurz H, van Helden P, Hoal E, Tromp G, Kinnear C, Kleynhans L, Glanzmann B, van Schalkwyk L, Miller M, Möller M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 2022; 12:14979. [PMID: 36056068 PMCID: PMC9440078 DOI: 10.1038/s41598-022-19025-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
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Affiliation(s)
- Christina Meiring
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Louis van Schalkwyk
- Department of Agriculture, Land Reform and Rural Development, PO Box 12, Skukuza, 1350, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
| | - Michele Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Private bag X1, Merriman Avenue, Stellenbosch, 7600, South Africa
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Nishida S, Mimura K, Mori H, Chiba S. Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina. BMC Res Notes 2022; 15:255. [PMID: 35842672 PMCID: PMC9288687 DOI: 10.1186/s13104-022-06147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
Objective Mandarina is an endangered land snail genus of the oceanic Ogasawara archipelago. On Chichijima Island, the largest inhabited island in Ogasawara, this genus is almost extinct in the wild due to predation by invasive species. Although ex situ conservation programs started in 2010, genetic diversity and population structure remain unclear due to a lack of genetic markers with sufficient genetic variation. In this study, we designed polymorphic microsatellite markers of Mandarina to enable genetic analysis and to develop appropriate conservation plans. Results Twenty-three polymorphic microsatellite markers were identified from the genomic DNA of wild samples of Mandarina mandarina. We assessed the genetic diversity of each marker. In 16 markers, neither linkage disequilibrium nor deviation from Hardy–Weinberg equilibrium was detected. These 16 markers were tested for multiplex PCR using low-density DNA extracted non-lethally from captive samples of M. mandarina, M. chichijimana and M. suenoae. Of the 16 markers, 15, 12 and 9 were usable for multiplex PCR, respectively. Genetic analysis using these microsatellite loci will be an important resource for the conservation of Mandarina. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06147-4.
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Affiliation(s)
- Shu Nishida
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Kotaro Mimura
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Hideaki Mori
- Japan Wildlife Research Center, Kotobashi 3-3-7 Sumida-ku Tokyo, Tokyo, 130-8606, Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,Center for Northeast Asian Studies, Tohoku University, 12-2, Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
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Tóth Z, Mahr K, Ölveczki G, Őri L, Lendvai ÁZ. Food Restriction Reveals Individual Differences in Insulin-Like Growth Factor-1 Reaction Norms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.826968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Most organisms have to cope with unpredictable environmental challenges such as fluctuations in nutritional resources. Insulin-like growth factor-1 (IGF-1) is an evolutionarily conserved hormone that is highly sensitive to the individual nutritional status and regulates major life-history traits including lifespan and reproduction across vertebrates. We investigated the role of IGF-1 during periods of food shortages by altering between two feeding regimes (110 and 70% of daily food intake) after a period of ad libitum feeding in captive bearded reedlings (Panurus biarmicus). Each dietary treatment was repeated twice. Birds lost mass under food restriction, but the magnitude of mass change depended on the preceding dietary conditions. Moreover, bearded reedlings showed large, repeatable individual differences in their IGF-1 reaction norms with some individuals increasing IGF-1 levels in response to a restricted diet, whereas others showed no responses or decreased IGF-1 levels. This variation was explained by differences in average body mass: heavier individuals had higher IGF-1 levels during the control treatment and were more likely to decrease IGF-1 levels in response to the dietary restriction than did lighter ones. This result uncovers an individual by environment interaction (I × E) and may have important implications for the evolution of IGF-1 related hormonal phenotypes in this species.
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Pinanga palms revisited 20 years on: what can changes in Pinanga species populations tell us about rainforest understory palm persistence? JOURNAL OF TROPICAL ECOLOGY 2022. [DOI: 10.1017/s0266467422000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Borneo is the centre of diversity of the palm genus Pinanga. At least 13 understory species have been recorded in the Ulu Temburong National Park in Brunei, but little is known of their persistence. Changes in populations of Pinanga understory palms may be indicative of more widespread changes due to climate change, such as changes in rainfall, which may be important for the palm diversity in the protected area. However, we know little about the population dynamics of these palms, how persistent their populations are or if they behave similarly over long time frames. In 1998, populations of five co-occurring species of Pinanga at several locations in the Ulu Temburong National Park were documented. This project aimed to undertake a comprehensive resurvey of the original five Pinanga palm species populations in order to assess if they showed similar population changes across sites and species after two decades. Overall, most species maintained their population size in the surveyed region but not consistently among sites, and one species significantly declined in abundance. There was considerable variation in population growth rate (R) within and among species and sites that was significantly correlated with density and the percentage of multi-stemmed plants. There was evidence of pulsed recruitment in some species and or sites rather than steady or exponential patterns of population growth.
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Diversity of the MHC class II DRB gene in the wolverine (Carnivora: Mustelidae: Gulo gulo) in Finland. PLoS One 2022; 17:e0267609. [PMID: 35536786 PMCID: PMC9089919 DOI: 10.1371/journal.pone.0267609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
The wolverine (Gulo gulo) in Finland has undergone significant population declines in the past. Since major histocompatibility complex (MHC) genes encode proteins involved in pathogen recognition, the diversity of these genes provides insights into the immunological fitness of regional populations. We sequenced 862 amplicons (242 bp) of MHC class II DRB exon 2 from 32 Finnish wolverines and identified 11 functional alleles and three pseudogenes. A molecular phylogenetic analysis indicated trans-species polymorphism, and PAML and MEME analyses indicated positive selection, suggesting that the Finnish wolverine DRB genes have evolved under balancing and positive selection. In contrast to DRB gene analyses in other species, allele frequencies in the Finnish wolverines clearly indicated the existence of two regional subpopulations, congruent with previous studies based on neutral genetic markers. In the Finnish wolverine, rapid population declines in the past have promoted genetic drift, resulting in a lower genetic diversity of DRB loci, including fewer alleles and positively selected sites, than other mustelid species analyzed previously. Our data suggest that the MHC region in the Finnish wolverine population was likely affected by a recent bottleneck.
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Jørgensen DB, Ørsted M, Kristensen TN. Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster. J Evol Biol 2022; 35:868-878. [PMID: 35532930 PMCID: PMC9325394 DOI: 10.1111/jeb.14015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour-a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4 . Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.
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Affiliation(s)
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg E, Denmark.,Department of Biology, Aarhus University, Aarhus C, Denmark
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15
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Buckley SJ, Brauer CJ, Unmack PJ, Hammer MP, Beheregaray LB. Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change. BMC Ecol Evol 2022; 22:35. [PMID: 35317750 PMCID: PMC8941757 DOI: 10.1186/s12862-022-01990-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations. RESULTS Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species. CONCLUSION Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, 0801, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia.
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Farmer NA, Doerr JC. Limiting factors for queen conch (Lobatus gigas) reproduction: A simulation-based evaluation. PLoS One 2022; 17:e0251219. [PMID: 35263325 PMCID: PMC8906866 DOI: 10.1371/journal.pone.0251219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
Queen conch are among the most economically, socially, and culturally important fishery resources in the Caribbean. Despite a multitude of fisheries management measures enacted across the region, populations are depleted and failing to recover. It is believed that queen conch are highly susceptible to depensatory processes, impacting reproductive success and contributing to the lack of recovery. We developed a model of reproductive dynamics to evaluate how variations in biological factors such as population density, movement speeds, rest periods between mating events, scent tracking, visual perception of conspecifics, sexual facilitation, and barriers to movement affect reproductive success and overall reproductive output. We compared simulation results to empirical observations of mating and spawning frequencies from conch populations in the central Bahamas and Florida Keys. Our results confirm that low probability of mate finding associated with decreased population density is the primary driver behind observed breeding behavior in the field, but is insufficient to explain observed trends. Specifically, sexual facilitation coupled with differences in movement speeds and ability to perceive conspecifics may explain the observed lack of mating at low densities and differences between mating frequencies in the central Bahamas and Florida Keys, respectively. Our simulations suggest that effective management strategies for queen conch should aim to protect high-density reproductive aggregations and critical breeding habitats.
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Affiliation(s)
- Nicholas A. Farmer
- NOAA Fisheries Southeast Regional Office, St. Petersburg, Florida, United States of America
| | - Jennifer C. Doerr
- NOAA Fisheries Southeast Fisheries Science Center, Galveston, Texas, United States of America
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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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López-Cortegano E, Moreno E, García-Dorado A. Genetic purging in captive endangered ungulates with extremely low effective population sizes. Heredity (Edinb) 2021; 127:433-442. [PMID: 34584227 PMCID: PMC8551332 DOI: 10.1038/s41437-021-00473-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.
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Affiliation(s)
- Eugenio López-Cortegano
- grid.4305.20000 0004 1936 7988Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
| | - Eulalia Moreno
- grid.466639.80000 0004 0547 1725Estación Experimental de Zonas Áridas (CSIC), 04120 Almería, Spain
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Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
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20
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Berger DJ, Crellen T, Lamberton PHL, Allan F, Tracey A, Noonan JD, Kabatereine NB, Tukahebwa EM, Adriko M, Holroyd N, Webster JP, Berriman M, Cotton JA. Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration. Nat Commun 2021; 12:4776. [PMID: 34362894 PMCID: PMC8346512 DOI: 10.1038/s41467-021-24958-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Control and elimination of the parasitic disease schistosomiasis relies on mass administration of praziquantel. Whilst these programmes reduce infection prevalence and intensity, their impact on parasite transmission and evolution is poorly understood. Here we examine the genomic impact of repeated mass drug administration on Schistosoma mansoni populations with documented reduced praziquantel efficacy. We sequenced whole-genomes of 198 S. mansoni larvae from 34 Ugandan children from regions with contrasting praziquantel exposure. Parasites infecting children from Lake Victoria, a transmission hotspot, form a diverse panmictic population. A single round of treatment did not reduce this diversity with no apparent population contraction caused by long-term praziquantel use. We find evidence of positive selection acting on members of gene families previously implicated in praziquantel action, but detect no high frequency functionally impactful variants. As efforts to eliminate schistosomiasis intensify, our study provides a foundation for genomic surveillance of this major human parasite.
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Affiliation(s)
- Duncan J Berger
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
| | - Thomas Crellen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Poppy H L Lamberton
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Institute for Biodiversity, Animal Health, and Comparative Medicine, and Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Fiona Allan
- The Natural History Museum, Department of Life Sciences, London, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jennifer D Noonan
- Institute of Parasitology, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Narcis B Kabatereine
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Edridah M Tukahebwa
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Moses Adriko
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Joanne P Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK.
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
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21
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Hardouin EA, Butler H, Cvitanović M, Ulrich RG, Schulze V, Schilling AK, Lurz PWW, Meredith A, Hodder KH. Wildlife conservation in a fragmented landscape: the Eurasian red squirrel on the Isle of Wight. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01380-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIsland populations may have a higher extinction risk due to reduced genetic diversity and need to be managed effectively in order to reduce the risk of biodiversity loss. The Eurasian red squirrels (Sciurus vulgaris) in the south of England only survive on three islands (the Isle of Wight, Brownsea and Furzey islands), with the Isle of Wight harbouring the largest population in the region. Fourteen microsatellites were used to determine the genetic structure of red squirrel populations on the Isle of Wight, as well as their relatedness to other populations of the species. Our results demonstrated that squirrels on these islands were less genetically diverse than those in Continental mainland populations, as would be expected. It also confirmed previous results from mitochondrial DNA which indicated that the squirrels on the Isle of Wight were relatively closely related to Brownsea island squirrels in the south of England. Importantly, our findings showed that genetic mixing between squirrels in the east and west of the Isle of Wight was very limited. Given the potential deleterious effects of small population size on genetic health, landscape management to encourage dispersal of squirrels between these populations should be a priority.
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22
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Rahimi O, Ohana‐Levi N, Brauner H, Inbar N, Hübner S, Drori E. Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range. Ecol Evol 2021; 11:6657-6671. [PMID: 34141248 PMCID: PMC8207413 DOI: 10.1002/ece3.7519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.
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Affiliation(s)
- Oshrit Rahimi
- Department of Chemical EngineeringAriel UniversityArielIsrael
| | | | - Hodaya Brauner
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
| | - Nimrod Inbar
- Department of Civil EngineeringAriel UniversityArielIsrael
- The Department of Geophysics and Space ScienceEastern Regional R&D CenterArielIsrael
| | - Sariel Hübner
- Galilee Research Institute (Migal)Tel‐Hai Academic CollegeUpper GalileeIsrael
| | - Elyashiv Drori
- Department of Chemical EngineeringAriel UniversityArielIsrael
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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Salmonella Infection in Turtles: A Risk for Staff Involved in Wildlife Management? Animals (Basel) 2021; 11:ani11061529. [PMID: 34073932 PMCID: PMC8225080 DOI: 10.3390/ani11061529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The aim of this study was to investigate the occurrence of non-typhoidal Salmonella in the turtles housed in a regional wildlife rescue centre of Apulia, in southern Italy, to assess the presence of Salmonella serovars that may represent a risk for operators involved in wildlife management. Sixty-nine tortoises, of which 36 were males and 33 were females, belonging to different species (Testudo hermanni hermanni, T. h. boettgeri, T. graeca, and T. marginata) were tested. All the turtles were adults (34 between 6 and 10 years of age and 35 more than 10 years of age). Salmonella was statistically detected more frequently in T. hermanni hermanni. No differences of the infection prevalence related to animal gender or age were found. Two different species, S. enterica and S. bongori, three S. enterica subspecies (enterica, diarizonae, salamae), and five different serovars (Hermannswerder, Abony, Ferruch, Richmond, Vancouver) within the group S. enterica subspecies enterica were identified. Two Salmonella types with different combinations were simultaneously found in specimens of T. h. hermanni. Most of the detected Salmonella types may represent a potential risk for operators in wildlife rescue centres. Abstract Monitoring of infections that may be transmitted to humans by animals in wildlife rescue centres is very important in order to protect the staff engaged in rehabilitation practices. Salmonella may be a natural inhabitant of the intestinal tract of turtles, rarely causing disease. This may represent a potential risk for humans, increasing the sanitary risk for operators in wildlife rescue centres. In this paper, the occurrence of non-typhoidal Salmonella among terrestrial turtles housed in a wildlife rescue centre in Southern Italy was investigated, in order to assess the serovars more frequently carried by turtles and identify those that may represent a risk for operators involved in wildlife management. Sixty-nine adult turtles (Testudo hermanni hermanni, T. h. boettgeri, T. graeca, and T. marginata) were tested. Detection and serotyping of Salmonella strains were performed according to ISO 6579-1 and ISO/TR 6579-3:2013, respectively. The distribution of Salmonella spp. was significantly higher in T. hermanni hermanni than in other species, independent of the age and gender of the animals. Two different Salmonella species, S. enterica and S. bongori, three S. enterica subspecies (enterica, diarizonae, salamae), and five different serovars (Hermannswerder, Abony, Ferruch, Richmond, Vancouver) within the group S. enterica subspecies enterica were identified. Different combinations of Salmonella types were simultaneously found in specimens of T. h. hermanni. Most of detected Salmonella types may represent a potential risk for public health. Adopting correct animal husbandry procedures and informing on potential sanitary risks may be useful for minimising the risk of transmission of Salmonella to workers involved in wildlife management.
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Blanco G, Morinha F. Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture. PeerJ 2021; 9:e11139. [PMID: 33828925 PMCID: PMC8005290 DOI: 10.7717/peerj.11139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 11/20/2022] Open
Abstract
The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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Nelson SL, Taylor SA, Reuter JD. An isolated white-tailed deer ( Odocoileus virginianus) population on St. John, US Virgin Islands shows low inbreeding and comparable heterozygosity to other larger populations. Ecol Evol 2021; 11:2775-2781. [PMID: 33767835 PMCID: PMC7981213 DOI: 10.1002/ece3.7230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
This is the first study to document the genetic diversity of the white-tailed deer population on St. John, US Virgin Islands. The island population was founded by a small number of animals, has very limited hunting or predation, and recently experienced a reduction in size following an extended drought in 2015. DNA samples were collected from hair from 23 anesthetized adult deer (13 males, 10 females) ranging in age from 1 to 8 years (3.36 ± 1.9 years) and also from fecal DNA samples, for a total of 42 individuals analyzed for genetic diversity. The St. John deer data set averaged 4.19 alleles per marker and demonstrates the second lowest number of alleles (A) when compared to other populations of Odocoileus virginianus (4.19). Heterozygosity was similar to the other studies (0.54) with little evidence of inbreeding. To explain the level of heterozygosity and level of inbreeding within the St. John population, three hypotheses are proposed, including the effect of intrinsic biological traits within the population, a recent infusion of highly heterogeneous loci from North American populations, and a consistent level of immigration from a nearby island. Additional work is needed to further understand the genetic history of the St. John and regional deer populations.
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Affiliation(s)
- Suzanne L. Nelson
- Department of Integrative PhysiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Scott A. Taylor
- Department of Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderCOUSA
| | - Jon D. Reuter
- Office of Animal ResourcesDepartment of Psychology and NeuroscienceUniversity of Colorado BoulderBoulderCOUSA
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Lewis RC, Pointer MD, Friend LA, Vasudeva R, Bemrose J, Sutter A, Gage MJG, Spurgin LG. Polyandry provides reproductive and genetic benefits in colonising populations. Ecol Evol 2020; 10:10851-10857. [PMID: 33072300 PMCID: PMC7548180 DOI: 10.1002/ece3.6742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 11/10/2022] Open
Abstract
Polyandry, when females mate with more than one male, is theorised to play an important role in successful colonisation of new habitats. In addition to possible benefits from sexual selection, even mild polyandry could facilitate colonisation by protecting against inbreeding and reducing the costs of mating with incompatible or infertile males. Here, we measure the importance of mild polyandry for population viability and reproductive fitness following experimental founder events into a higher‐temperature regime. Using colonisation experiments with the model beetle Tribolium castaneum, in which females can produce offspring for up to 140 days following a single mating, we founded more than 100 replicate populations using single females that had been given the opportunity to mate with either one or two males and then tracked their subsequent population dynamics. Following population viability and fitness across 10 generations, we found that extinction rates were significantly lower in populations founded by females given polyandrous opportunities to mate with two males (9%) compared to populations founded by monogamous females (34%). In addition, populations founded by females that had been provided with opportunities to store sperm from two different males showed double the median productivity following colonisation compared to monogamous‐founded populations. Notably, we identified short‐term and longer‐term benefits to post‐colonisation populations from double‐mating, with results suggesting that polyandry acts to both protect against mating with incompatible males through the founder event, and reduce inbreeding depression as the colonisation proceeds for 10 generations. Our results therefore show that even mild polyandry provides both reproductive and genetic benefits for colonising populations.
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Affiliation(s)
- Rebecca C Lewis
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Michael D Pointer
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Lucy A Friend
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Ramakrishnan Vasudeva
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - James Bemrose
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Andreas Sutter
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Matthew J G Gage
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
| | - Lewis G Spurgin
- School of Biological Sciences Norwich Research Park University of East Anglia Norwich UK
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Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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García J, Morán‐Ordóñez A, García JT, Calero‐Riestra M, Alda F, Sanz J, Suárez‐Seoane S. Current landscape attributes and landscape stability in breeding grounds explain genetic differentiation in a long‐distance migratory bird. Anim Conserv 2020. [DOI: 10.1111/acv.12616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. García
- Department of Biodiversity and Environmental Management University of León León Spain
| | | | - J. T. García
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - M. Calero‐Riestra
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - F. Alda
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga TN USA
| | - J. Sanz
- Laboratorio de Teledetección de la Universidad de Valladolid (LATUV) Valladolid Spain
| | - S. Suárez‐Seoane
- Department of Organisms and Systems Biology (BOS: Ecology Unit) Research Unit of Biodiversity (UMIBUO‐CSIC‐PA)University of Oviedo Oviedo Spain
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31
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Unravelling effects of grazing intensity on genetic diversity and fitness of desert vegetation. Perspect Ecol Conserv 2020. [DOI: 10.1016/j.pecon.2020.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral theory explained how selection competes with random fixation dynamics that produce molecular clocks essential e.g. for dating evolutionary histories. However, quantitative proteomics revealed that selection pressures not relating to optimal function play much larger roles than previously thought, acting perhaps most importantly via protein expression levels. This paper first summarizes recent progress in the 21st century toward recovering this universal selection pressure. Then, the paper argues that proteome cost minimization is the dominant, underlying 'non-function' selection pressure controlling most of the evolution of already functionally adapted living systems. A theory of proteome cost minimization is described and argued to have consequences for understanding evolutionary trade-offs, aging, cancer, and neurodegenerative protein-misfolding diseases.
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Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gauthier J, Pajkovic M, Neuenschwander S, Kaila L, Schmid S, Orlando L, Alvarez N. Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Mol Ecol Resour 2020; 20:1191-1205. [PMID: 32304133 PMCID: PMC7540272 DOI: 10.1111/1755-0998.13167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022]
Abstract
Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.
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Affiliation(s)
| | - Mila Pajkovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Finland
| | - Sarah Schmid
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ludovic Orlando
- Laboratoire AMIS CNRS UMR 5288, Faculté de Médecine de Purpan, Toulouse, France.,Globe Institut, Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Ham-Dueñas JG, Canales-del-Castillo R, Voelker G, Ruvalcaba-Ortega I, Aguirre-Calderón CE, González-Rojas JI. Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi). PLoS One 2020; 15:e0232282. [PMID: 32352998 PMCID: PMC7192469 DOI: 10.1371/journal.pone.0232282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.
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Affiliation(s)
- José G. Ham-Dueñas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | - Ricardo Canales-del-Castillo
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Biodiversity Research and Teaching Collections, Texas A&M University, College Station, Texas, United States of America
| | - Irene Ruvalcaba-Ortega
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | | | - José I. González-Rojas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
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Prôa M, Nanova O. Severe population bottleneck and cranial morphology change in the Mednyi Island subspecies of Arctic fox Vulpes lagopus (Carnivora: Canidae). MAMMALIA 2020. [DOI: 10.1515/mammalia-2018-0165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Arctic foxes, Vulpes lagopus living on Mednyi Island suffered a drastic decline in population size in the late 1970s due to an outbreak of mange epizootic. This dramatic fall in numbers rendered the subspecies endangered, and the concomitant loss of variability resulted in a population bottleneck. Here, we investigate whether differences in cranial morphology between Mednyi Island Arctic foxes and Bering Island Arctic foxes could be attributed to the severe population bottleneck suffered by the Mednyi population in the 1970s. We used morphometric traits as proxies for genetic data to provide estimates of FST. Results show higher FST estimates for the Mednyi population than for the Bering population, which we interpret as a bottleneck signature. FST results also indicate a pattern of divergence between the two populations consistent with random genetic drift. Bottleneck detection is critical for the interpretation of the demographic history of the endangered Mednyi Island Arctic fox, with consequences for conservation management.
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Affiliation(s)
- Miguel Prôa
- Centro de Investigação em Antropologia e Saúde, Departamento de Ciências da Vida , Universidade de Coimbra , Apartado 3046 , 3001-401 Coimbra , Portugal
| | - Olga Nanova
- Zoological Museum , M.V. Lomonosov Moscow State University , Bol’shaya Nikitskaya, 2 , Moscow 125009 , Russia
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37
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Shapcott A, James H, Simmons L, Shimizu Y, Gardiner L, Rabehevitra D, Letsara R, Cable S, Dransfield J, Baker WJ, Rakotoarinivo M. Population modelling and genetics of a critically endangered Madagascan palm Tahina spectabilis. Ecol Evol 2020; 10:3120-3137. [PMID: 32211182 PMCID: PMC7083664 DOI: 10.1002/ece3.6137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/26/2020] [Accepted: 02/07/2020] [Indexed: 11/10/2022] Open
Abstract
Madagascar is home to 208 indigenous palm species, almost all of them endemic and >80% of which are endangered. We undertook complete population census and sampling for genetic analysis of a relatively recently discovered giant fan palm, the Critically Endangered Tahina spectablis in 2008 and 2016. Our 2016 study included newly discovered populations and added to our genetic study. We incorporated these new populations into species distribution niche model (SDM) and projected these onto maps of the region. We developed population matrix models based on observed demographic data to model population change and predict the species vulnerability to extinction by undertaking population viability analysis (PVA). We investigated the potential conservation value of reintroduced planted populations within the species potential suitable habitat. We found that the population studied in 2008 had grown in size due to seedling regeneration but had declined in the number of reproductively mature plants, and we were able to estimate that the species reproduces and dies after approximately 70 years. Our models suggest that if the habitat where it resides continues to be protected the species is unlikely to go extinct due to inherent population decline and that it will likely experience significant population growth after approximately 80 years due to the reproductive and life cycle attributes of the species. The newly discovered populations contain more genetic diversity than the first discovered southern population which is genetically depauperate. The species appears to demonstrate a pattern of dispersal leading to isolated founder plants which may eventually lead to population development depending on local establishment opportunities. The conservation efforts currently put in place including the reintroduction of plants within the species potential suitable habitat if maintained are thought likely to enable the species to sustain itself but it remains vulnerable to anthropogenic impacts.
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Affiliation(s)
- Alison Shapcott
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Heather James
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Laura Simmons
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Yoko Shimizu
- Genecology Research Centre School of Science and Engineering University of the Sunshine Coast Maroochydore Qld Australia
| | - Lauren Gardiner
- Cambridge University Herbarium Department of Plant Sciences University of Cambridge Cambridge UK
| | | | - Rokiman Letsara
- Parc Botanique et Zoologique deTsimbazaza Antananarivo Madagascar
| | | | | | | | - Mijoro Rakotoarinivo
- Département de Biologie et Ecologie Végétales Faculté des Sciences Université d'Antananarivo Antananarivo Madagascar
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38
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Arauco-Shapiro G, Schumacher KI, Boersma D, Bouzat JL. The role of demographic history and selection in shaping genetic diversity of the Galápagos penguin (Spheniscus mendiculus). PLoS One 2020; 15:e0226439. [PMID: 31910443 PMCID: PMC6946592 DOI: 10.1371/journal.pone.0226439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/26/2019] [Indexed: 11/25/2022] Open
Abstract
Although many studies have documented the effects of demographic bottlenecks on the genetic diversity of natural populations, there is conflicting evidence of the roles that genetic drift and selection may play in driving changes in genetic variation at adaptive loci. We analyzed genetic variation at microsatellite and mitochondrial loci in conjunction with an adaptive MHC class II locus in the Galápagos penguin (Spheniscus mendiculus), a species that has undergone serial demographic bottlenecks associated with El Niño events through its evolutionary history. We compared levels of variation in the Galápagos penguin to those of its congener, the Magellanic penguin (Spheniscus magellanicus), which has consistently maintained a large population size and thus was used as a non-bottlenecked control. The comparison of neutral and adaptive markers in these two demographically distinct species allowed assessment of the potential role of balancing selection in maintaining levels of MHC variation during bottleneck events. Our analysis suggests that the lack of genetic diversity at both neutral and adaptive loci in the Galápagos penguin likely resulted from its restricted range, relatively low abundance, and history of demographic bottlenecks. The Galápagos penguin revealed two MHC alleles, one mitochondrial haplotype, and six alleles across five microsatellite loci, which represents only a small fraction of the diversity detected in Magellanic penguins. Despite the decreased genetic diversity in the Galápagos penguin, results revealed signals of balancing selection at the MHC, which suggest that selection can mitigate some of the effects of genetic drift during bottleneck events. Although Galápagos penguin populations have persisted for a long time, increased frequency of El Niño events due to global climate change, as well as the low diversity exhibited at immunological loci, may put this species at further risk of extinction.
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Affiliation(s)
- Gabriella Arauco-Shapiro
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Katelyn I. Schumacher
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Dee Boersma
- Center for Ecosystem Sentinels and Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Juan L. Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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39
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Loureiro LO, Engstrom MD, Lim BK. Comparative phylogeography of mainland and insular species of Neotropical molossid bats ( Molossus). Ecol Evol 2020; 10:389-409. [PMID: 31993120 PMCID: PMC6972955 DOI: 10.1002/ece3.5903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype-by-sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.
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Affiliation(s)
- Livia O. Loureiro
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Mark D. Engstrom
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoONCanada
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40
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Klerks PL, Athrey GN, Leberg PL. Response to Selection for Increased Heat Tolerance in a Small Fish Species, With the Response Decreased by a Population Bottleneck. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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41
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Ørsted M, Hoffmann AA, Sverrisdóttir E, Nielsen KL, Kristensen TN. Genomic variation predicts adaptive evolutionary responses better than population bottleneck history. PLoS Genet 2019; 15:e1008205. [PMID: 31188830 PMCID: PMC6590832 DOI: 10.1371/journal.pgen.1008205] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 06/24/2019] [Accepted: 05/20/2019] [Indexed: 11/18/2022] Open
Abstract
The relationship between population size, inbreeding, loss of genetic variation and evolutionary potential of fitness traits is still unresolved, and large-scale empirical studies testing theoretical expectations are surprisingly scarce. Here we present a highly replicated experimental evolution setup with 120 lines of Drosophila melanogaster having experienced inbreeding caused by low population size for a variable number of generations. Genetic variation in inbred lines and in outbred control lines was assessed by genotyping-by-sequencing (GBS) of pooled samples consisting of 15 males per line. All lines were reared on a novel stressful medium for 10 generations during which body mass, productivity, and extinctions were scored in each generation. In addition, we investigated egg-to-adult viability in the benign and the stressful environments before and after rearing at the stressful conditions for 10 generations. We found strong positive correlations between levels of genetic variation and evolutionary response in all investigated traits, and showed that genomic variation was more informative in predicting evolutionary responses than population history reflected by expected inbreeding levels. We also found that lines with lower genetic diversity were at greater risk of extinction. For viability, the results suggested a trade-off in the costs of adapting to the stressful environments when tested in a benign environment. This work presents convincing support for long-standing evolutionary theory, and it provides novel insights into the association between genetic variation and evolutionary capacity in a gradient of diversity rather than dichotomous inbred/outbred groups.
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Affiliation(s)
- Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg E, Denmark
- Bio21 Molecular Science and Biotechnology Institute, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ary Anthony Hoffmann
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg E, Denmark
- Bio21 Molecular Science and Biotechnology Institute, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Elsa Sverrisdóttir
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg E, Denmark
| | - Kåre Lehmann Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg E, Denmark
| | - Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej, Aalborg E, Denmark
- Department of Bioscience, Aarhus University, Ny Munkegade, Aarhus C, Denmark
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Thompson LM, Klütsch CFC, Manseau M, Wilson PJ. Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction. Ecol Evol 2019; 9:7030-7046. [PMID: 31380031 PMCID: PMC6662424 DOI: 10.1002/ece3.5269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R ST and F ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad-scale patterns of genetic structure and closely aligned with the R ST network. The F ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.
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Affiliation(s)
- Laura M. Thompson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
U.S. Geological SurveyNational Climate Adaptation Science CenterRestonVirginia
| | - Cornelya F. C. Klütsch
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Present address:
Division of Environmental Research in the Barents RegionNorwegian Institute of Bioeconomy Research (NIBIO)SvanvikNorway
| | - Micheline Manseau
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
- Landscape Science and TechnologyEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Paul J. Wilson
- Natural Resources DNA Profiling and Forensic CentreTrent UniversityPeterboroughOntarioCanada
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The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01992-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Marrero MV, Oostermeijer G, Nogales M, Van Hengstum T, Saro I, Carqué E, Sosa PA, Bañares Á. Comprehensive population viability study of a rare endemic shrub from the high mountain zone of the Canary Islands and its conservation implications. J Nat Conserv 2019. [DOI: 10.1016/j.jnc.2018.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Feng S, Fang Q, Barnett R, Li C, Han S, Kuhlwilm M, Zhou L, Pan H, Deng Y, Chen G, Gamauf A, Woog F, Prys-Jones R, Marques-Bonet T, Gilbert MTP, Zhang G. The Genomic Footprints of the Fall and Recovery of the Crested Ibis. Curr Biol 2019; 29:340-349.e7. [PMID: 30639104 PMCID: PMC6345625 DOI: 10.1016/j.cub.2018.12.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/09/2018] [Accepted: 12/06/2018] [Indexed: 01/19/2023]
Abstract
Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
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Affiliation(s)
- Shaohong Feng
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qi Fang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; The Francis Crick Institute, London NW1 1AT, UK
| | - Sojung Han
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hailin Pan
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Guangji Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Anita Gamauf
- Museum of Natural History Vienna, 1st Zoological Department - Ornithology, Burgring 7, A-1010 Vienna, Austria
| | - Friederike Woog
- Staatliches Museum für Naturkunde, Rosenstein 1, 70191 Stuttgart, Germany
| | - Robert Prys-Jones
- Bird Group, Department of Life Sciences, Natural History Museum, Akeman St, Tring, Herts HP23 6AP, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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47
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Mito N, Ohshima K, Saitoh O. Genetic Diversity among Clouded Salamanders (Hynobius nebulosus) in Shiga Prefecture. Zoolog Sci 2018; 35:427-435. [PMID: 30298788 DOI: 10.2108/zs170095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Japanese clouded salamander (Hynobius nebulosus) is a lentic-breeding species distributed throughout western Japan. Threats, such as habitat loss, have led to it being categorized as a vulnerable species. To explore the phylogeographic features and population differentiation among clouded salamanders in Shiga prefecture, we analyzed sequences of the mitochondrial cytochrome b gene. DNA samples were collected from 29 distinct breeding sites, and 53 cytochrome b haplotypes were identified. On the basis of comparison of the composition and frequency of haplotypes in each breeding site, salamanders in each habitat appeared to have distinct characteristics. Significant genetic differentiation was observed in 93.3% of possible pairs of habitats in Shiga prefecture, and 67.7% of habitat pairs within the same locality were found to be significantly different. These results suggest that the salamanders' poor locomotion combined with topographic effects may have contributed to the diversity of locally distributed salamanders in Shiga. Phylogenetic analysis showed that haplotypes of H. nebulosus in Shiga can be divided into five groups (the Nagahama-Maibara group, Otsu group, Konan group 1, Konan group 2, and Takashima group), each with a distinct geographical distribution. Haplotypes of the Otsu group, however, were exceptionally widely distributed. The results of the present study will contribute to the future of H. nebulosus conservation management in Shiga.
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Affiliation(s)
- Naoki Mito
- 1 Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan
| | - Kazuhiko Ohshima
- Department of Computer Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan
| | - Osamu Saitoh
- 1 Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama-shi, Shiga 526-0829, Japan
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48
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Borovski T, Tadmor-Levi R, Shapiro J, Rubinstein G, Agyakwah SK, Hulata G, David L. Historical and recent reductions in genetic variation of the Sarotherodon galilaeus population in the Sea of Galilee. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1102-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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49
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Velie BD, Jäderkvist Fegraeus K, Ihler CF, Lindgren G, Strand E. Competition lifespan survival analysis in the Norwegian‐Swedish Coldblooded Trotter racehorse. Equine Vet J 2018; 51:206-211. [DOI: 10.1111/evj.12989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/02/2018] [Indexed: 11/29/2022]
Affiliation(s)
- B. D. Velie
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - K. Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - C. F. Ihler
- Department of Companion Animal Clinical Sciences Faculty of Veterinary Medicine Norwegian University of Life Sciences Oslo Norway
| | - G. Lindgren
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - E. Strand
- Department of Companion Animal Clinical Sciences Faculty of Veterinary Medicine Norwegian University of Life Sciences Oslo Norway
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Successful re-establishment of a rabbit population from embryos vitrified 15 years ago: The importance of biobanks in livestock conservation. PLoS One 2018; 13:e0199234. [PMID: 29912976 PMCID: PMC6005500 DOI: 10.1371/journal.pone.0199234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 06/04/2018] [Indexed: 01/02/2023] Open
Abstract
Genetic resource banks (GRB) are a valuable tool for maintaining genetic variability and preserving breeds from pathogens or catastrophe, enabling us to assess and correct breeding schemes, minimizing the impact of genetic drift and facilitating diffusion. This study tests their efficiency in re-establishing two extinct populations of a synthetic rabbit line selected for daily weight gain, using vitrified embryos from two generations (18th and 36th) separated by 15 years of genetic selection. The effect of long-term storage of vitrified embryos in liquid nitrogen was also evaluated. A total of 516 vitrified embryos using the same protocol were transferred into 54 recipients. The embryos had been maintained in liquid nitrogen during 2 different periods, (i) 1 year (301 embryos and 26 transfers, 36th generation) and (ii) 15 years (259 embryos and 28 transfers, 18th generation). A total of 80.0% (8/10 to 18th) and 60.0% (9/15 to 36th) of the foundational sire families were eventually re-established. Over approximately one year, animals within each population were crossed to produce the next generation and re-establish the original population size. Our study demonstrated that our GRB of embryos vitrified 15 years ago is a successful strategy to re-establish rabbit populations to continue the breeding programme.
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