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Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [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: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
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Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
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2
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Dehasque M, Morales HE, Díez-Del-Molino D, Pečnerová P, Chacón-Duque JC, Kanellidou F, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Nikolskiy P, Danilov GK, Giannì M, van der Sluis L, Higham T, Heintzman PD, Oskolkov N, Gilbert MTP, Götherström A, van der Valk T, Vartanyan S, Dalén L. Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell 2024:S0092-8674(24)00577-4. [PMID: 38942016 DOI: 10.1016/j.cell.2024.05.033] [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: 10/02/2023] [Revised: 02/08/2024] [Accepted: 05/17/2024] [Indexed: 06/30/2024]
Abstract
A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Héloïse Muller
- Master de Biologie, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon I, Universite de Lyon, 69007 Lyon, France
| | - Valerii Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Albert Protopopov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 3 University Embankment, Box 199034, Saint-Petersburg, Russia
| | - Maddalena Giannì
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Laura van der Sluis
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Peter D Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; SciLifeLab, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
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3
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Sochor M, Šarhanová P, Duchoslav M, Konečná M, Hroneš M, Trávníček B. Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles. ANNALS OF BOTANY 2024; 134:163-178. [PMID: 38549558 PMCID: PMC11161565 DOI: 10.1093/aob/mcae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND AND AIMS Rubus ser. Glandulosi provides a unique model of geographical parthenogenesis on a homoploid (2n = 4x) level. We aim to characterize evolutionary and phylogeographical patterns in this taxon and shed light on the geographical differentiation of apomicts and sexuals. Ultimately, we aim to evaluate the importance of phylogeography in the formation of geographical parthenogenesis. METHODS Rubus ser. Glandulosi was sampled across its Eurasian range together with other co-occurring Rubus taxa (587 individuals in total). Double-digest restriction site-associated DNA sequencing (ddRADseq) and modelling of suitable climate were used for evolutionary inferences. KEY RESULTS Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. Sexuals were introgressed from Rubus dolichocarpus and Rubus moschus in West Asia and from Rubus ulmifolius agg., Rubus canescens and Rubus incanescens in Europe, whereas apomicts were characterized by alleles of Rubus subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as was occasional hybridization with other taxa. CONCLUSIONS We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France, whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographical parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts, and maladaptive population genetic processes probably did not shape the geographical patterns.
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Affiliation(s)
- Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, 783 71 Olomouc, Czech Republic
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petra Šarhanová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Martin Duchoslav
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Konečná
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michal Hroneš
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Bohumil Trávníček
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Kreling SES, Reese EM, Cavalluzzi OM, Bozzi NB, Messinger R, Schell CJ, Long RA, Prugh LR. City divided: Unveiling family ties and genetic structuring of coyotes in Seattle. Mol Ecol 2024:e17427. [PMID: 38837263 DOI: 10.1111/mec.17427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non-urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.
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Affiliation(s)
- Samantha E S Kreling
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Ellen M Reese
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Olivia M Cavalluzzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Natalee B Bozzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Riley Messinger
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, California, USA
| | | | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
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Paijmans AJ, Berthelsen AL, Nagel R, Christaller F, Kröcker N, Forcada J, Hoffman JI. Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups. Sci Rep 2024; 14:12610. [PMID: 38824161 PMCID: PMC11144264 DOI: 10.1038/s41598-024-62290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024] Open
Abstract
Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We investigated inbreeding effects in a declining population of Antarctic fur seals (Arctocephalus gazella) at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal's staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother-offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits. This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.
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Affiliation(s)
- A J Paijmans
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany.
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - A L Berthelsen
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - R Nagel
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Centre for Biological Diversity, University of St. Andrews, St Andrews, KY16 9TH, UK
| | - F Christaller
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - N Kröcker
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - J Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - J I Hoffman
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
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Laurent R, Gineau L, Utge J, Lafosse S, Phoeung CL, Hegay T, Olaso R, Boland A, Deleuze JF, Toupance B, Heyer E, Leutenegger AL, Chaix R. Measuring the Efficiency of Purging by non-random Mating in Human Populations. Mol Biol Evol 2024; 41:msae094. [PMID: 38839045 PMCID: PMC11184347 DOI: 10.1093/molbev/msae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.
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Affiliation(s)
- Romain Laurent
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Laure Gineau
- IRD, MERIT, Université Paris Cité, 75006 Paris, France
| | - José Utge
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Sophie Lafosse
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Tatyana Hegay
- Laboratory of Genome-cell technology, Institute of Immunology and Human genomics, Academy of Sciences, Tashkent, Uzbekistan
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Bruno Toupance
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
- Eco-Anthropologie, Université Paris Cité, 75006 Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Raphaëlle Chaix
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
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Giovannini S, Chessari G, Riggio S, Marletta D, Sardina MT, Mastrangelo S, Sarti FM. Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed. Front Genet 2024; 15:1379086. [PMID: 38881792 PMCID: PMC11176520 DOI: 10.3389/fgene.2024.1379086] [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: 01/30/2024] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Local livestock breeds play a crucial role in global biodiversity, connecting natural and human-influenced environments and contributing significantly to ecosystem services. While commercial breeds dominate industrial systems, local livestock breeds in developing countries, like Barbarine sheep in Tunisia, are vital for food security and community maintenance. The Tunisian Barbarine sheep, known for its adaptability and distinctive fat-tailed morphology, faces challenges due to historical crossbreeding. In this study, the Illumina Ovine SNP50K BeadChip array was used to perform a genome-wide characterization of Tunisian Barbarine sheep to investigate its genetic diversity, the genome structure, and the relationship within the context of Mediterranean breeds. The results show moderate genetic diversity and low inbreeding. Runs of Homozygosity analysis find genomic regions linked to important traits, including fat tail characteristics. Genomic relationship analysis shows proximity to Algerian thin-tailed breeds, suggesting crossbreeding impacts. Admixture analysis reveals unique genetic patterns, emphasizing the Tunisian Barbarine's identity within the Mediterranean context and its closeness to African breeds. Current results represent a starting point for the creation of monitoring and conservation plans. In summary, despite genetic dilution due to crossbreeding, the identification of genomic regions offers crucial insights for conservation. The study confirms the importance of preserving unique genetic characteristics of local breeds, particularly in the face of ongoing crossbreeding practices and environmental challenges. These findings contribute valuable insights for the sustainable management of this unique genetic reservoir, supporting local economies and preserving sheep species biodiversity.
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Affiliation(s)
- Samira Giovannini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
| | - Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Perugia, Italy
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Lavanchy E, Weir BS, Goudet J. Detecting inbreeding depression in structured populations. Proc Natl Acad Sci U S A 2024; 121:e2315780121. [PMID: 38687793 PMCID: PMC11087799 DOI: 10.1073/pnas.2315780121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.
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Affiliation(s)
- Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne1015, Switzerland
- Population Genetics and Genomics group, Swiss Institute of Bioinformatics, University of Lausanne, LausanneCH-1015, Switzerland
| | - Bruce S. Weir
- Department of Biostatistics, University of Washington, SeattleWA98195
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne1015, Switzerland
- Population Genetics and Genomics group, Swiss Institute of Bioinformatics, University of Lausanne, LausanneCH-1015, Switzerland
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Al Hikmani H, van Oosterhout C, Birley T, Labisko J, Jackson HA, Spalton A, Tollington S, Groombridge JJ. Can genetic rescue help save Arabia's last big cat? Evol Appl 2024; 17:e13701. [PMID: 38784837 PMCID: PMC11113348 DOI: 10.1111/eva.13701] [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: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
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Affiliation(s)
- Hadi Al Hikmani
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Office for Conservation of the EnvironmentDiwan of Royal CourtMuscatOman
- The Royal Commission for AlUlaAlUlaSaudi Arabia
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Thomas Birley
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Centre for Biodiversity and Environment Research, Research Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Island Biodiversity and Conservation CentreUniversity of SeychellesVictoriaSeychelles
- Department of Life SciencesThe Natural History MuseumLondonUK
| | - Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| | | | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- School of Animal Rural and Environmental SciencesNottingham Trent UniversityNottinghamUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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11
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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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12
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Cox-Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii). Mol Ecol 2024:e17362. [PMID: 38682494 DOI: 10.1111/mec.17362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Karah Cox-Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
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13
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Fu Q, Zhou J, Luan S, Dai P, Lyu D, Chen B, Luo K, Kong J, Meng X. Analysis of Elimination Effects of Inbreeding on Genotype Frequency in Larval Stages of Chinese Shrimp. BIOLOGY 2024; 13:268. [PMID: 38666880 PMCID: PMC11047943 DOI: 10.3390/biology13040268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.
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Affiliation(s)
- Qiang Fu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Jingxin Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Sheng Luan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Ping Dai
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Ding Lyu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Baolong Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kun Luo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Jie Kong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Xianhong Meng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.F.); (J.Z.); (S.L.); (P.D.); (D.L.); (B.C.); (K.L.); (J.K.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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14
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Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
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Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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15
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Hoelzel AR, Gkafas GA, Kang H, Sarigol F, Le Boeuf B, Costa DP, Beltran RS, Reiter J, Robinson PW, McInerney N, Seim I, Sun S, Fan G, Li S. Genomics of post-bottleneck recovery in the northern elephant seal. Nat Ecol Evol 2024; 8:686-694. [PMID: 38383849 PMCID: PMC11009102 DOI: 10.1038/s41559-024-02337-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence. Recovery was rapid and now there are over 200,000 individuals. We sequenced 260 modern and 8 historical northern elephant seal nuclear genomes to assess the impact of the population bottleneck on individual northern elephant seals and to better understand their recovery. Here we show that inbreeding, an increase in the frequency of alleles compromised by lost function, and allele frequency distortion, reduced the fitness of breeding males and females, as well as the performance of adult females on foraging migrations. We provide a detailed investigation of the impact of a severe bottleneck on fitness at the genomic level and report on the role of specific gene systems.
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Affiliation(s)
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Burney Le Boeuf
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Daniel P Costa
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Roxanne S Beltran
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Joanne Reiter
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Patrick W Robinson
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Nancy McInerney
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | | | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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16
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Pacheco C, Rio-Maior H, Nakamura M, Álvares F, Godinho R. Relatedness-based mate choice and female philopatry: inbreeding trends of wolf packs in a human-dominated landscape. Heredity (Edinb) 2024; 132:211-220. [PMID: 38472424 PMCID: PMC10997798 DOI: 10.1038/s41437-024-00676-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Inbreeding can reduce offspring fitness and has substantial implications for the genetic diversity and long-term viability of populations. In social cooperative canids, inbreeding is conditioned by the geographic proximity between opposite-sex kin outside natal groups and the presence of related individuals in neighbouring groups. Consequently, challenges in moving into other regions where the species is present can also affect inbreeding rates. These can be particularly problematic in areas of high human density, where movement can be restricted, even for highly vagile species. In this study, we investigate the socio-ecological dynamics of Iberian wolf packs in the human-dominated landscape of Alto Minho, in northwest Portugal, where wolves exhibit a high prevalence of short-distance dispersal and limited gene flow with neighbouring regions. We hypothesise that mating occurs regardless of relatedness, resulting in recurrent inbreeding due to high kin encounter rates. Using data from a 10-year non-invasive genetic monitoring programme and a combination of relatedness estimates and genealogical reconstructions, we describe genetic diversity, mate choice, and dispersal strategies among Alto Minho packs. In contrast with expectations, our findings reveal relatedness-based mate choice, low kin encounter rates, and a reduced number of inbreeding events. We observed a high prevalence of philopatry, particularly among female breeders, with the most common breeding strategy involving the pairing of a philopatric female with an unrelated immigrant male. Overall, wolves were not inbred, and temporal changes in genetic diversity were not significant. Our findings are discussed, considering the demographic trend of wolves in Alto Minho and its human-dominated landscape.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
| | - Helena Rio-Maior
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Mónia Nakamura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Francisco Álvares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
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17
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Zhang W, Lin K, Fu W, Xie J, Fan X, Zhang M, Luo H, Yin Y, Guo Q, Huang H, Chen T, Lin X, Yuan Y, Huang C, Du S. Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey. Genes (Basel) 2024; 15:398. [PMID: 38674333 PMCID: PMC11049310 DOI: 10.3390/genes15040398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.
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Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan 364201, China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu 611830, China;
| | - Hongxing Luo
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Qiang Guo
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Tengteng Chen
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Xipan Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Cheng Huang
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
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18
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Siddique A, Shahid N, Liess M. Revealing the cascade of pesticide effects from gene to community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170472. [PMID: 38296075 DOI: 10.1016/j.scitotenv.2024.170472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Global pesticide exposure in agriculture leads to biodiversity loss, even at ultra-low concentrations below the legal limits. The mechanisms by which the effects of toxicants act at such low concentrations are still unclear, particularly in relation to their propagation across the different biological levels. In this study, we demonstrate, for the first time, a cascade of effects from the gene to the community level. At the gene level, agricultural pesticide exposure resulted in reduced genetic diversity of field-collected Gammarus pulex, a dominant freshwater crustacean in Europe. Additionally, we identified alleles associated with adaptations to pesticide contamination. At the individual level, this genetic adaptation to pesticides was linked to a lower fecundity, indicating related fitness costs. At the community level, the combined effect of pesticides and competitors caused a decline in the overall number and abundance of pesticides susceptible macroinvertebrate competing with gammarids. The resulting reduction in interspecific competition provided an advantage for pesticide-adapted G. pulex to dominate macroinvertebrate communities in contaminated areas, despite their reduced fitness due to adaptation. These processes demonstrate the complex cascade of effects, and also illustrate the resilience and adaptability of biological systems across organisational levels to meet the challenges of a changing environment.
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Affiliation(s)
- Ayesha Siddique
- Department System-Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Naeem Shahid
- Department System-Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, 61100 Vehari, Pakistan.
| | - Matthias Liess
- Department System-Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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19
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Renoirt M, Angelier F, Cheron M, Jabaud L, Tartu S, Brischoux F. Population declines of a widespread amphibian in agricultural landscapes. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:17. [PMID: 38498200 DOI: 10.1007/s00114-024-01905-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
Modern agricultural practices are suspected to play a major role in the ongoing erosion of biodiversity. In order to assess whether this biodiversity loss is linked to past habitat modifications (e.g. land consolidation) or to current consequences of modern agriculture (e.g. use of agrochemicals), it remains essential to monitor species that have persisted in agricultural landscapes to date. In this study, we assessed the presence, abundance and recent population trends of one such species, the spined toad (Bufo spinosus) along a gradient of habitats from preserved (forests) to highly agricultural sites in rural Western France. Our results showed that both presence and abundance of spined toads were markedly lower in reproductive ponds surrounded by intensive agriculture. The most salient result of our study is the ongoing decline of this species in farmland habitats. Indeed, this result suggests that unknown factors are currently affecting a widespread terrestrial amphibian previously thought to persist in agricultural landscapes. These factors have recently induced strong population declines over the course of a few years. Future investigations are required to identify these factors at a time when anthropogenic activities are currently leading to unprecedented rates of biodiversity loss.
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Affiliation(s)
- Matthias Renoirt
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France
| | - Frédéric Angelier
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France
| | - Marion Cheron
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France
| | - Laure Jabaud
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France
| | - Sabrina Tartu
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France
| | - François Brischoux
- Centre d'Etudes Biologiques de Chizé, UMR7372 CNRS-La Rochelle Université, 79360, Villiers en Bois, France.
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20
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Grundei LL, Schöttes FM, Gethöffer F, Tost D, Kluge L, Siebert U, Pees M. Human-Wildlife Interaction-A Social Survey. Animals (Basel) 2024; 14:808. [PMID: 38473194 DOI: 10.3390/ani14050808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
With the results of a survey presented in this paper, we provide insight into public attitudes towards dealing with wildlife. Based on 1569 data sets derived from participating stakeholders, we inquired about the individual experience the participants had made with wild animals, and asked about their personal engagement, attitude towards management, and emotions involved and tried to evaluate basic contextual knowledge. As a result, we discovered a positive effect showing that a strong opinion about dealing with wildlife is associated with increasing contextual knowledge. People that are experienced in and engaged in wildlife conservation expressed significantly stronger positive emotions in this context. We conclude that education is essential in dealing with wildlife responsibly and that positive emotions are a main trigger for such engagement. The results of the survey underline that a combination of contextual knowledge and a positive attitude towards wildlife leads to a higher awareness of possible conflicts between humans and wildlife. Furthermore, these criteria are crucial when developing strategies that strive for a sustainable coexistence.
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Affiliation(s)
- Lara-Luisa Grundei
- Department of Small Mammal, Reptile and Avian Medicine and Surgery, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hanover, Germany
| | - Franziska M Schöttes
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Friederike Gethöffer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Daniel Tost
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Laurin Kluge
- Department of Small Mammal, Reptile and Avian Medicine and Surgery, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hanover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Michael Pees
- Department of Small Mammal, Reptile and Avian Medicine and Surgery, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hanover, Germany
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21
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [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] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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22
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Roffler GH, Pilgrim KL, Williams BC. Patterns of Wolf Dispersal Respond to Harvest Density across an Island Complex. Animals (Basel) 2024; 14:622. [PMID: 38396590 PMCID: PMC10885989 DOI: 10.3390/ani14040622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Wolves are highly mobile predators and can disperse across a variety of habitats and over long distances. However, less is known about dispersal capabilities across water and among islands. The biogeography of island systems fosters spatially structured local populations, and their degree of connectivity may influence the dynamics and long-term viability of the regional population. We sought to quantify wolf dispersal rate, distance, and dispersal sex bias throughout Prince of Wales Island, a 6670 km2 island in southeast Alaska, and the surrounding islands that constitute the wildlife management unit (9025 km2). We also investigated patterns of dispersal in relation to hunting and trapping intensity and wolf population density. We used DNA data collected during 2012-2021 long-term monitoring efforts and genotyped 811 wolves, 144 of which (18%) were dispersers. Annual dispersal rates were 9-23% and had a weakly positive relationship with wolf density. Wolves dispersed 41.9 km on average (SD = 23.7 km), and males and females did not disperse at different rates. Of the dispersing wolves, 107 died, and the majority (n = 81) died before they were able to settle. The leading manner of death was trapping (97% of mortalities), and wolves tended to disperse from areas with low harvest density to areas where harvest density was relatively higher. Dispersal occurred both to and from small islands and the larger Prince of Wales Island, indicating bidirectional as opposed to asymmetrical movement, and the genetic overlap of wolf groups demonstrates connectivity throughout this naturally patchy system. Island ecosystems have different predator-prey dynamics and recolonization processes than large, intact systems due to their isolation and restricted sizes; thus, a better understanding of the degree of population connectivity including dispersal patterns among islands in the Prince of Wales archipelago could help inform the management and research strategies of these wolves.
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Affiliation(s)
- Gretchen H. Roffler
- Alaska Department of Fish and Game, Division of Wildlife Conservation, Douglas, AK 99824, USA
| | - Kristine L. Pilgrim
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, MT 59802, USA;
| | - Benjamin C. Williams
- Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK 99801, USA;
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23
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Fleischer R, Eibner GJ, Schwensow NI, Pirzer F, Paraskevopoulou S, Mayer G, Corman VM, Drosten C, Wilhelm K, Heni AC, Sommer S, Schmid DW. Immunogenetic-pathogen networks shrink in Tome's spiny rat, a generalist rodent inhabiting disturbed landscapes. Commun Biol 2024; 7:169. [PMID: 38341501 PMCID: PMC10858909 DOI: 10.1038/s42003-024-05870-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Anthropogenic disturbance may increase the emergence of zoonoses. Especially generalists that cope with disturbance and live in close contact with humans and livestock may become reservoirs of zoonotic pathogens. Yet, whether anthropogenic disturbance modifies host-pathogen co-evolutionary relationships in generalists is unknown. We assessed pathogen diversity, neutral genome-wide diversity (SNPs) and adaptive MHC class II diversity in a rodent generalist inhabiting three lowland rainforest landscapes with varying anthropogenic disturbance, and determined which MHC alleles co-occurred more frequently with 13 gastrointestinal nematodes, blood trypanosomes, and four viruses. Pathogen-specific selection pressures varied between landscapes. Genome-wide diversity declined with the degree of disturbance, while MHC diversity was only reduced in the most disturbed landscape. Furthermore, pristine forest landscapes had more functional important MHC-pathogen associations when compared to disturbed forests. We show co-evolutionary links between host and pathogens impoverished in human-disturbed landscapes. This underscores that parasite-mediated selection might change even in generalist species following human disturbance which in turn may facilitate host switching and the emergence of zoonoses.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Georg Joachim Eibner
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nina Isabell Schwensow
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Fabian Pirzer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Gerd Mayer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Robert Koch Institute, Nordufer 20, Berlin, 13353, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Robert Koch Institute, Nordufer 20, Berlin, 13353, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Alexander Christoph Heni
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.
| | - Dominik Werner Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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24
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Patterson C, Pilakouta N. Effects of Parental Care on the Magnitude of Inbreeding Depression: A Meta-Analysis in Fishes. Am Nat 2024; 203:E50-E62. [PMID: 38306289 DOI: 10.1086/728001] [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] [Indexed: 02/04/2024]
Abstract
AbstractInbreeding results from matings between relatives and often leads to a reduction in the fitness of inbred offspring, known as inbreeding depression. There is substantial variation in the magnitude of inbreeding depression among and within species, driven by differences in the biotic and abiotic environment. Recent studies in three species found that parental care has the potential to buffer against inbreeding depression in the offspring, but the generality of this pattern is still unknown. Here, we performed a meta-analysis to test whether variation in the magnitude of inbreeding depression is related to among-species differences in parental care in fishes. We synthesized 536 effect sizes across 56 studies and 18 species, spanning 47 years of research. We found that inbred offspring suffer a smaller reduction in fitness in species that provide biparental care than in species with uniparental or no care. By using a comparative approach, this study provides novel insights into the capacity of parental care to moderate inbreeding depression and suggests that these effects may currently be underappreciated. Considering the potential effects of parental care on inbreeding depression can help us understand why some species avoid inbreeding, whereas others tolerate or even prefer inbreeding, which has important implications for the maintenance of genetic variation within populations.
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25
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Xu X, Wang C, Xu C, Yuan J, Wang G, Wu Y, Huang C, Jing H, Yang P, Xu L, Peng S, Shan F, Xia X, Jin F, Hou F, Wang J, Mi D, Ren Y, Liu Y, Irwin DM, Li X, Chen W, Li G. Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 2024; 24:e13896. [PMID: 37955396 DOI: 10.1111/1755-0998.13896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
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Affiliation(s)
- Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yajiang Wu
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shiming Peng
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Xiaochao Xia
- Guangdong Wildlife Monitoring, Rescue and Conservation Center, Guangzhou, China
| | - Fuyuan Jin
- Guangdong Maoming Forest Park Administrative Office, Maoming, China
| | - Fanghui Hou
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an, China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Guangzhou Zoo, Guangzhou, China
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26
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Jirabanjongjit A, Traiperm P, Rattanamanee C, Stewart AB. Near extinct Argyreia versicolor and rare Argyreia mekongensis are dependent on carpenter bee pollinators. AOB PLANTS 2024; 16:plae001. [PMID: 38352178 PMCID: PMC10862652 DOI: 10.1093/aobpla/plae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
Argyreia versicolor and Argyreia mekongensis are extremely rare plant species. The former had not been seen for nearly 100 years until two individuals were found in Thailand in 2018, and only a handful of populations are known for the latter. The aims of this study were to examine the breeding systems of A. versicolor and A. mekongensis using pollination experiments and to determine their potential pollinators via floral observations. Our controlled pollination experiments uncovered the self-incompatibility of both species. Pollinator censuses indicated that females of two carpenter bee species, Xylocopa aestuans and Xylocopa latipes, were the predominant floral visitors for both Argyreia species. Our observations confirmed a harmonious match between the floral shape of both Argyreia species and the body sizes of these pollinators, ensuring effective pollen transfer and validating their role as putative pollinators. In line with the high frequency of pollinator visits observed, our controlled pollination experiments found no evidence of pollen limitation under field conditions. The findings of this study hold significance for the conservation of these endangered species, yet the situation is dire for A. versicolor, with one of the two individuals under study recently lost. Hence, it is crucial to intensify monitoring efforts for the species, aiming to identify additional individuals for potential inclusion in an ex-situ conservation program. Simultaneously, safeguarding the habitat of these plant species and their pollinators will be critical.
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Affiliation(s)
- Awapa Jirabanjongjit
- M.Sc. Program in Plant Sciences, Faculty of Graduate Studies, Mahidol University, Nakhon Pathom 73170, Thailand
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Paweena Traiperm
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Alyssa B Stewart
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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27
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Manawaduge CG, Ryan J, Phillips MJ, Fuller S. Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia. Ecol Evol 2024; 14:e10895. [PMID: 38333093 PMCID: PMC10850812 DOI: 10.1002/ece3.10895] [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: 07/24/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024] Open
Abstract
Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among N. lloydii populations. Therefore, we undertook a genome-wide single nucleotide polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south-eastern Queensland. Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that N. lloydii produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un-bagged flowering and fruiting rates, and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of N. lloydii are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.
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Affiliation(s)
- Chapa G. Manawaduge
- School of Biology and Environmental SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
- Present address:
CSIROHealth and BiosecurityActonACTAustralia
| | - James Ryan
- School of Biology and Environmental SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Matthew J. Phillips
- School of Biology and Environmental SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Susan Fuller
- School of Biology and Environmental SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
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28
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577275. [PMID: 38352393 PMCID: PMC10862700 DOI: 10.1101/2024.01.26.577275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Karah Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
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29
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Freudiger A, Jovanovic VM, Huang Y, Snyder-Mackler N, Conrad DF, Miller B, Montague MJ, Westphal H, Stadler PF, Bley S, Horvath JE, Brent LJN, Platt ML, Ruiz-Lambides A, Tung J, Nowick K, Ringbauer H, Widdig A. Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574911. [PMID: 38260273 PMCID: PMC10802400 DOI: 10.1101/2024.01.09.574911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.
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Affiliation(s)
- Annika Freudiger
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vladimir M Jovanovic
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Noah Snyder-Mackler
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hendrikje Westphal
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, Santa Fe, NM, USA
| | - Stefanie Bley
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julie E Horvath
- Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina, Durham, USA
- Research and Collections Section, North Carolina Museum of Natural Sciences, North Carolina, Raleigh, USA
- Department of Biological Sciences, North Carolina State University, North Carolina, Raleigh, USA
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, the Wharton School of Business, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Angelina Ruiz-Lambides
- Cayo Santiago Field Station, Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke University Population Research Institute, Durham, North Carolina, USA
| | - Katja Nowick
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Widdig
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
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30
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Iglesias-Carrasco M, Taboada B, Lozano M, Carazo P, Garcia-Roa R, Rodriguez-Exposito E, Garcia-Gonzalez F. Sexual selection buffers the negative consequences of population fragmentation on adaptive plastic responses to increasing temperatures. Evolution 2024; 78:86-97. [PMID: 37888875 DOI: 10.1093/evolut/qpad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
Whether sexual selection facilitates or hampers the ability to plastically respond to novel environments might depend on population structure, via its effects on sexual interactions and associated fitness payoffs. Using experimentally evolved lines of the seed beetle Callosobruchus maculatus, we tested whether individuals evolving under different sexual selection (monogamy vs. polygamy) and population spatial structure (metapopulation vs. undivided populations) treatments differed in their response across developmental thermal conditions (control, hot, or stressful) in a range of fitness and fitness-associated traits. We found that individuals from subdivided populations had lower lifetime reproductive success at hot temperatures, but only in lines evolving under relaxed sexual selection, revealing a complex interaction between sexual selection, population structure, and thermal environmental stress on fitness. We also found an effect of population structure on several traits, including fertility and adult emergence success, under exposure to high thermal conditions. Finally, we found a strong negative effect of hot and stressful temperatures on fitness and associated traits. Our results show that population structure can exacerbate the impact of a warming climate, potentially leading to declines in population viability, but that sexual selection can buffer the negative influence of population subdivision on adaptation to warm temperatures.
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Affiliation(s)
- Maider Iglesias-Carrasco
- Evolution and Ecology of Sexual Interactions Group, Doñana Biological Station-CSIC, Seville, Spain
| | - Beatriz Taboada
- Evolution and Ecology of Sexual Interactions Group, Doñana Biological Station-CSIC, Seville, Spain
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Miguel Lozano
- Evolution and Ecology of Sexual Interactions Group, Doñana Biological Station-CSIC, Seville, Spain
| | - Pau Carazo
- Ecology, Ethology and Evolution Group, Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valenica, Spain
| | | | | | - Francisco Garcia-Gonzalez
- Evolution and Ecology of Sexual Interactions Group, Doñana Biological Station-CSIC, Seville, Spain
- Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, Australia
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31
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Nagy I, Nguyen TA. Characterizing and Eliminating the Inbreeding Load. Vet Sci 2023; 11:8. [PMID: 38250914 PMCID: PMC10819885 DOI: 10.3390/vetsci11010008] [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: 10/29/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.
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Affiliation(s)
- István Nagy
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary;
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32
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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33
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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34
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Pröhl H, Rodríguez A. Importance of Genetic-Fitness Correlations for the Conservation of Amphibians. Animals (Basel) 2023; 13:3564. [PMID: 38003181 PMCID: PMC10668650 DOI: 10.3390/ani13223564] [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: 10/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Endangered animals suffer from isolation of their habitats. Isolation leads to a reduction in population size as well as a decrease in genetic diversity and a concomitant increase in the risk of extinction. Amphibians are the most endangered vertebrate class. Besides habitat loss, fragmentation and isolation, amphibians are threatened by emerging diseases e.g., chytrid fungus or Ranavirus. By employing experiments, researchers investigate whether changes in genetic diversity within or among isolated populations affect amphibian fitness. While genetic diversity estimates are based on molecular markers, typically microsatellites, fitness is mostly measured as tadpole performance in rearing experiments often under varying environmental conditions. Tadpole performances (e.g., body mass, growth rate and survival) have been found to be negatively affected by low genetic diversity, as several studies have found a positive association between genetic diversity and these fitness traits. Moreover, infection with pathogens also seems to be more likely in individuals or populations with lower genetic diversity. Overall, these genetic-fitness correlations seem to be more pronounced or detectable in smaller, declining populations but not in larger populations. Genomic studies, which sample a larger fraction of the genome, are still scarce in the conservation genetic literature on amphibians. These are likely to increase in upcoming years and may reveal adaptive variants that protect against dangerous pathogens or environmental changes. Altogether, genetic-fitness correlation studies should be a priority in order to develop effective management plans for the genetic rescue of isolated, imperilled amphibian populations.
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Affiliation(s)
- Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559 Hannover, Germany;
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35
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Buono V, Bissattini AM, Davoli F, Mengoni C, Mucci N, Vignoli L. Fine-scale spatial genetic structure and dispersal among Italian smooth newt populations in a rural landscape. Sci Rep 2023; 13:19956. [PMID: 37968502 PMCID: PMC10651844 DOI: 10.1038/s41598-023-47265-8] [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: 07/04/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023] Open
Abstract
Amphibians are particularly sensitive to habitat loss and fragmentation caused by the intensification and modernization of farming occurring in the second half of the twentieth century in the Mediterranean basin. However, artificial water bodies, associated with traditional husbandry, proved to be important surrogate for amphibian feeding and reproduction. Here, multilocus genotypes were used to investigate the spatial population structure of Lissotriton vulgaris meridionalis and the role of drinking troughs in supporting viable breeding populations within a rural landscape interested by traditional husbandry and agriculture. Our genetic analysis highlighted the conservation value and the potential stepping-stone function of artificial aquatic sites in the dispersal of the species and for the gene flow maintenance. Indeed, populations of drinking troughs show allelic richness and heterozygosity levels comparable to those from natural ponds and there is no great evidence of genetic bottlenecks. A complex system of artificial aquatic sites and few natural wetlands was identified sustaining a well-structured network of demes highly interconnected with themselves and natural aquatic sites. The conservation of the identified genetic clusters may be useful to prevent further population declines and future loss of genetic diversity within the study area characterized by scarce natural wetlands that frequently dried because of agricultural practices and strong seasonality. Site-specific protection measures are needed to contrast the progressive disappearance of drinking troughs observed in the last years in Italy because of the abandonment of traditional farming practices in favour of modern agriculture and intensive farming.
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Affiliation(s)
- Vincenzo Buono
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy.
| | | | - Francesca Davoli
- Unit for Conservation, Management and Sustainable Use of Marine Aquatic Resources (BIO-CIT), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Chiara Mengoni
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano Dell'Emilia, 40064, Bologna, Italy
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36
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Lobo D, López-Bao JV, Godinho R. The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach. Mol Ecol 2023; 32:5986-5999. [PMID: 37855673 DOI: 10.1111/mec.17171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
After decades of intense persecution, the Iberian wolf subspecies faced a severe bottleneck in the 1970s that considerably reduced its range and population size, nearly leading to its extinction in central and southern Iberian Peninsula. Such population decline could have impacted the genetic diversity of Iberian wolves through different processes, namely genetic drift and dynamics of hybridization with domestic dogs. By contrasting the genomes of 68 contemporary with 54 historical samples spanning the periods before and immediately after the 1970s bottleneck, we found evidence of its impact on genetic diversity and dynamics of wolf-dog hybridization. Our genome-wide assessment revealed that wolves and dogs form two well-differentiated genetic groups in Iberia and that hybridization rates did not increase during the bottleneck. However, an increased number of hybrid individuals was found over time during the population re-expansion, particularly at the edge of the wolf range. We estimated a low percentage of dog ancestry (~1.4%) in historical samples, suggesting that dog introgression was not a key driver for wolf extinction in central and southern Iberia. Our findings also unveil a significant decline in genetic diversity in contemporary samples, with the highest proportion of homozygous segments in the genome being recently inherited. Overall, our study provides unprecedented insight into the impact of a sharp decline on the Iberian wolf genome and refines our understanding of the ecological and evolutionary drivers of wolf-dog hybridization in the wild.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias) Oviedo University, Mieres, Spain
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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37
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Arana A, Esteves J, Ramírez R, Galetti PM, Pérez Z J, Ramirez JL. Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction. Sci Rep 2023; 13:18465. [PMID: 37891335 PMCID: PMC10611785 DOI: 10.1038/s41598-023-45715-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023] Open
Abstract
Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.
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Affiliation(s)
- Alejandra Arana
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Juan Esteves
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Rina Ramírez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - José Pérez Z
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru.
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38
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Dussex N, Tørresen OK, van der Valk T, Le Moullec M, Veiberg V, Tooming-Klunderud A, Skage M, Garmann-Aarhus B, Wood J, Rasmussen JA, Pedersen ÅØ, Martin SL, Røed KH, Jakobsen KS, Dalén L, Hansen BB, Martin MD. Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer. iScience 2023; 26:107811. [PMID: 37744038 PMCID: PMC10514459 DOI: 10.1016/j.isci.2023.107811] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/24/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Typically much smaller in number than their mainland counterparts, island populations are ideal systems to investigate genetic threats to small populations. The Svalbard reindeer (Rangifer tarandus platyrhynchus) is an endemic subspecies that colonized the Svalbard archipelago ca. 6,000-8,000 years ago and now shows numerous physiological and morphological adaptations to its arctic habitat. Here, we report a de-novo chromosome-level assembly for Svalbard reindeer and analyze 133 reindeer genomes spanning Svalbard and most of the species' Holarctic range, to examine the genomic consequences of long-term isolation and small population size in this insular subspecies. Empirical data, demographic reconstructions, and forward simulations show that long-term isolation and high inbreeding levels may have facilitated the reduction of highly deleterious-and to a lesser extent, moderately deleterious-variation. Our study indicates that long-term reduced genetic diversity did not preclude local adaptation to the High Arctic, suggesting that even severely bottlenecked populations can retain evolutionary potential.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Tom van der Valk
- Centre for PalaeoGenetics, Svante Arrhenius väg 20C, SE 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE 104 05 Stockholm, Sweden
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
| | - Vebjørn Veiberg
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), NO 7034 Trondheim, Trondheim, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Benedicte Garmann-Aarhus
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
- Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA Cambridge, UK
| | - Jacob A. Rasmussen
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
- Globe Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Sarah L.F. Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
| | - Knut H. Røed
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Love Dalén
- Centre for PalaeoGenetics, Svante Arrhenius väg 20C, SE 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brage B. Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), NO 7034 Trondheim, Trondheim, Norway
| | - Michael D. Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
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Liang HM, Yang KT, Cheng YT, Chang SC, Lin CY, Tsai MY, Lin DY, Hung KH. Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer ( Rusa unicolor swinhoei). Animals (Basel) 2023; 13:3106. [PMID: 37835712 PMCID: PMC10571969 DOI: 10.3390/ani13193106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of captive populations. In this study, 239 Formosan sambar deer were genotyped using 13 microsatellites to analyze their genetic diversity and population genetic structure. Our results indicate a high-resolution power of these microsatellites in individual discrimination and parentage analysis. However, captive populations exhibit a low level of genetic diversity, likely because of inbreeding and bottleneck effects. Both principal coordinate analysis (PCoA) and STRUCTURE analyses revealed two distinct and segregated genetic groups within the captive populations and indicated no clear population genetic structure among the captive populations. Introducing new genetic material from the wild through translocation offers a potential solution for mitigating the impact of inbreeding and enhancing genetic diversity. The comprehensive information obtained from these genetic analyses is crucial for the development of effective breeding strategies aimed at preserving and enhancing Formosan sambar deer populations.
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Affiliation(s)
- Hsiao-Mei Liang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Kuo-Tai Yang
- Department of Animal Science, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Yu-Tzu Cheng
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Shen-Chang Chang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Cheng-Yung Lin
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Ming-Yang Tsai
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Der-Yuh Lin
- Genetics and Physiology Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan;
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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40
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Gu TT, Wu H, Yang F, Gaubert P, Heighton SP, Fu Y, Liu K, Luo SJ, Zhang HR, Hu JY, Yu L. Genomic analysis reveals a cryptic pangolin species. Proc Natl Acad Sci U S A 2023; 120:e2304096120. [PMID: 37748052 PMCID: PMC10556634 DOI: 10.1073/pnas.2304096120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 09/27/2023] Open
Abstract
Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.
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Affiliation(s)
- Tong-Tong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto4450-208, Portugal
| | - Sean P. Heighton
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
| | - Yeyizhou Fu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Ke Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Hua-Rong Zhang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
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41
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Schenekar T, Weiss A, Weiss SJ. Applying molecular genetic data at different scales to support conservation assessment of European Habitats Directive listed species: A case study of Eurasian otter in Austria. Evol Appl 2023; 16:1735-1752. [PMID: 38020875 PMCID: PMC10660814 DOI: 10.1111/eva.13597] [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: 08/03/2022] [Revised: 08/08/2023] [Accepted: 09/04/2023] [Indexed: 12/01/2023] Open
Abstract
Evaluating intraspecific genetic structure and diversity is fundamental to assessing a species' conservation status, but direct incorporation of such information into legal frameworks such as the EU's Habitats Directive is surprisingly rare. How genetic structure aligns with EU member state boundaries or biogeographic regions may be very important in designing management plans or achieving legislative goals. The Eurasian fish otter experienced a sharp population decline during the 20th century but is currently re-expanding in several countries. The species is listed under Annex II and IV of the European Habitats Directive, and member states are obliged to assess the species separately across different biogeographic regions. We genotyped 2492 otter spraints across four provinces in Austria, collected between 2017 and 2021. A total of 384 different genotypes were identified, supporting densities along river habitats from 0.1 to 0.47 otters per river km (mean: 0.306), with a resampling-based simulation supporting limited density overestimation at survey lengths of 20 km or more. Three distinct genetic clusters were revealed, two of them presumably reflecting two relict populations whereas the source of the third cluster is unknown. The geographic extent of the three clusters does not coincide with provincial or biogeographic boundaries, both relevant for assessment and management within existing national or European legislative frameworks. We advocate more consideration of genetic structure in the assessment and conservation management planning of species listed in the European Habitats Directive.
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Affiliation(s)
| | - Andreas Weiss
- NASA Postdoctoral Program FellowNASA Goddard Space Flight CenterGreenbeltMarylandUSA
- Institute of PhysicsUniversity of GrazGrazAustria
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42
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Dussex N, Morales HE, Grossen C, Dalén L, van Oosterhout C. Purging and accumulation of genetic load in conservation. Trends Ecol Evol 2023; 38:961-969. [PMID: 37344276 DOI: 10.1016/j.tree.2023.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, NTNU University Museum, Erling Skakkes Gate 47A, 7012 Trondheim, Norway.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christine Grossen
- WSL Swiss Federal Research Institute, CH-8903 Birmensdorf, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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43
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Morgan EJ, Kaiser-Bunbury CN, Edwards PJ, Fleischer-Dogley F, Kettle CJ. Mate-choice for close kin is associated with improved offspring survival in Lodoicea maldivica, the largest-seeded plant in the world. Sci Rep 2023; 13:15305. [PMID: 37723314 PMCID: PMC10507110 DOI: 10.1038/s41598-023-41419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/26/2023] [Indexed: 09/20/2023] Open
Abstract
We studied spatial patterns of kinship in the offspring of the endangered Lodoicea maldivica, a dioecious palm that produces the largest seed of any plant. Previous research has suggested that restricted seed and pollen dispersal in populations resulted in strong spatial genetic structure. We used microsatellites to genotype young plants and their potential parents at four sites across the species' entire natural range. We determined the most likely parents of each young plant based on the spatial separation of each parent pair, their genetic relatedness, and the level of correlated paternity. We identified both parents (43 female, 54 male) for 139 of 493 young plants. Mean distance between parental pairs was 26.8 m. Correlated paternity was low (0.168), indicating that mother trees were often pollinated by several fathers. Parental pairs were more closely related than expected by chance, suggesting outbreeding depression. Our results highlight the apparent strong mate choice for close kin in parent pairs of surviving offspring. We discuss the alternative biological processes that could lead to this, including the potential for break-up of favourable allelic combinations necessary for the development of the palm's very large seed. Management implications include germinating seeds where they naturally fall, using a diverse range of male plants as pollen donors for hand pollination, and protecting the native community of gecko pollinators.
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Affiliation(s)
- Emma J Morgan
- ITES-Ecosystem Management, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland.
| | - Christopher N Kaiser-Bunbury
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, UK
| | - Peter J Edwards
- IBZ-Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | | | - Chris J Kettle
- ITES-Ecosystem Management, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland
- Bioversity International, Via di San Domenico 1, 00153, Rome, Italy
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44
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Hudson DW, McKinley TJ, Benton CH, Delahay R, McDonald RA, Hodgson DJ. Multi-locus homozygosity promotes actuarial senescence in a wild mammal. J Anim Ecol 2023; 92:1881-1892. [PMID: 37427855 DOI: 10.1111/1365-2656.13979] [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: 11/07/2022] [Accepted: 06/05/2023] [Indexed: 07/11/2023]
Abstract
Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.
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Affiliation(s)
- Dave W Hudson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Clare H Benton
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Richard Delahay
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Dave J Hodgson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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45
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Hoy SR, Hedrick PW, Peterson RO, Vucetich LM, Brzeski KE, Vucetich JA. The far-reaching effects of genetic process in a keystone predator species, grey wolves. SCIENCE ADVANCES 2023; 9:eadc8724. [PMID: 37611108 PMCID: PMC10446474 DOI: 10.1126/sciadv.adc8724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
Although detrimental genetic processes are known to adversely affect the viability of populations, little is known about how detrimental genetic processes in a keystone species can affect the functioning of ecosystems. Here, we assessed how changes in the genetic characteristics of a keystone predator, grey wolves, affected the ecosystem of Isle Royale National Park over two decades. Changes in the genetic characteristic of the wolf population associated with a genetic rescue event, followed by high levels of inbreeding, led to a rise and then fall in predation rates on moose, the primary prey of wolves and dominant mammalian herbivore in this system. Those changes in predation rate led to large fluctuations in moose abundance, which in turn affected browse rates on balsam fir, the dominant forage for moose during winter and an important boreal forest species. Thus, forest dynamics can be traced back to changes in the genetic characteristics of a predator population.
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Affiliation(s)
- Sarah R. Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | | | - Rolf O. Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - Leah M. Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - Kristin E. Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - John A. Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
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46
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Eberhardt M, Prochowska S, Partyka A, Bielas W, Van Soom A, Olech W, Niżański W. The morphology, morphometry and functionality of fresh and cryopreserved wisent (Bison bonasus) epididymal spermatozoa. Sci Rep 2023; 13:13866. [PMID: 37620548 PMCID: PMC10449768 DOI: 10.1038/s41598-023-40798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Epididymal spermatozoa obtained post mortem are considered a valuable source of genetic material which is often irrevocably lost. This makes these gametes constitute a key element in protection and restitution programs. The wisent (Bison bonasus, Linnaeus 1758) is a species that survived in zoos after extinction from its natural habitat. This resulted in a narrowing of the genetic pool of the whole population, which is at present derived from only 12 ancestors. Currently, wisent protection programs are aimed at preserving the genetic diversity by establishing a germplasm bank. The objective of this study was to comprehensively characterize the morphology, morphometry and functionality of wisent epididymal spermatozoa and evaluate the effectiveness of their cryopreservation in extender based on Tris buffer and chicken egg yolk. The median total number of spermatozoa obtained from one individual was 1985.0 × 106 (62.5 × 106-7452.0 × 106). These gametes were characterized by median: 40.0% (0.5-70.0%) subjective motility, 69.8% (32.5-90.0%) viability and 54.3% (10.5-83.3%) normal morphology. The sperm head had a median size of 5.0 μm (3.5-6.7 μm) width, 8.5 μm (6.4-11.3 μm) length and 36.9 μm2 (23.7-48.6 μm2) surface area. The viable population of the obtained gametes was characterized by median values 53.2% (4.5-80.3%) of intact sperm membrane, 50.8 (26.0-76.6%) of intact acrosome, 0.4% (0-98.7%) of fragmented chromatin, 5.9% (0.0-88.8%) of cells with high mitochondrial potential and 42.1% (8.3-63.7%) without lipid peroxidation. The viable population of the frozen/thawed gametes was characterized by median values: 18.4% (2.4-57.9%) of intact sperm membrane, 35.1 (11.9-56.7%) of intact acrosome, 0.07% (0-89.2%) of fragmented chromatin, 12.8% (0.0-49.7%) of cells with high mitochondrial potential and 16.3% (2.2-53.6%) without lipid peroxidation. Due to the material originating from a relatively large number of wild individuals, the research presented here contributed to the description of certain species standards for the assessment of wisent epididymal spermatozoa. The presented effect of cryopreservation on these gametes justifies the use of an extender based on Tris buffer with the addition of chicken egg yolk. The obtained effects are satisfactory from the point of view of preserving valuable genetic material and their use in ART.
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Affiliation(s)
- Maria Eberhardt
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366, Wrocław, Poland.
| | - Sylwia Prochowska
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366, Wrocław, Poland
| | - Agnieszka Partyka
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366, Wrocław, Poland
| | - Wiesław Bielas
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366, Wrocław, Poland
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Wanda Olech
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786, Warsaw, Poland
| | - Wojciech Niżański
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366, Wrocław, Poland.
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47
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Crossman CA, Fontaine MC, Frasier TR. A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales. Mol Ecol 2023. [PMID: 37577945 DOI: 10.1111/mec.17099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent- and identity-by-descent-based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne ) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome-wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome-wide datasets to help resolve long-standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long-term small Ne , low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps.
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Affiliation(s)
- Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 224), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Timothy R Frasier
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
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48
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Liu P, Li G, Zhao N, Song X, Wang J, Shi X, Wang B, Zhang L, Dong L, Li Q, Liu Q, Lu L. Neutral Forces and Balancing Selection Interplay to Shape the Major Histocompatibility Complex Spatial Patterns in the Striped Hamster in Inner Mongolia: Suggestive of Broad-Scale Local Adaptation. Genes (Basel) 2023; 14:1500. [PMID: 37510404 PMCID: PMC10379431 DOI: 10.3390/genes14071500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces. METHODS In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes. RESULTS We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two. CONCLUSIONS Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.
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Affiliation(s)
- Pengbo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Guichang Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ning Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xinfei Shi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Bin Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Public Health School, Jiamusi University, Jiamusi 154007, China
| | - Lu Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Dong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Qingduo Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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49
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Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
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Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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50
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Ash E, Cushman S, Kaszta Ż, Landguth E, Redford T, Macdonald DW. Female-biased introductions produce higher predicted population size and genetic diversity in simulations of a small, isolated tiger (Panthera tigris) population. Sci Rep 2023; 13:11199. [PMID: 37433862 DOI: 10.1038/s41598-023-36849-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/11/2023] [Indexed: 07/13/2023] Open
Abstract
Isolation of wildlife populations represents a key conservation challenge in the twenty-first century. This may necessitate consideration of translocations to ensure population viability. We investigated the potential population and genetic trajectory of a small, isolated tiger (Panthera tigris) population in Thailand's Dong Phayayen-Khao Yai forest complex across a range of scenarios. Using an individual-based, spatially-explicit population modelling approach, we simulate population and genetic trajectories and evaluate the relative impact of translocations from a related population. Population and genetic trajectories in our study were most sensitive to sex and number of individuals translocated and translocation frequency. Translocation of females produced consistently higher population, allelic richness, and heterozygosity compared to equal numbers of males. Despite population increases, declines in allelic richness and heterozygosity across simulations were stark, with simulations predicting a mean decline of allelic richness and heterozygosity of 46.5% and 53.5% without intervention, respectively. Translocations of four females every generation or every other generation were required to prevent substantial heterozygosity declines. While translocations could increase population size, they may fail to prevent long-term loss of genetic diversity in small populations unless applied frequently. This reinforces the importance of incorporating realistic processes of genetic inheritance and gene flow in modelling small populations.
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Affiliation(s)
- Eric Ash
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK.
| | - Samuel Cushman
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
| | - Żaneta Kaszta
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
- Department of Biological Sciences, Northern Arizona University, 617 S Beaver, Flagstaff, AZ, 86011, USA
| | - Erin Landguth
- School of Public and Community Health Sciences, Center for Population Health Research, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Tim Redford
- Freeland Foundation, Lumpini Ville Phahon-Sutthisan, 23/90 7th Floor, Bldg. B, Sutthisan Winitchai Rd., Samsen Nai, Phaya Thai, Bangkok, 10400, Thailand
| | - David W Macdonald
- Wildlife Conservation Research Unit, Department of Biology, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Tubney, OX13 5QL, Oxon, UK
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