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McCreesh K, Guthrie AL, Spiro S, Patterson S. A SYSTEMATIC REVIEW OF RETROSPECTIVE MORBIDITY AND MORTALITY STUDIES ON CAPTIVE WILDLIFE SPECIES. J Zoo Wildl Med 2024; 55:1-12. [PMID: 38453482 DOI: 10.1638/2023-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 03/09/2024] Open
Abstract
Zoological institutions manage animals for conservation, education, entertainment, and research purposes. Zoological staff have a responsibility to safeguard the welfare of animals in their care. Retrospective morbidity and/or mortality studies (MMSs) can be useful tools to highlight common diseases in captive wildlife populations. There is currently no standardized methodology for conducting MMSs. Variation in the methodology of MMSs, particularly the categorization of diseases, can make comparisons between studies challenging and may limit the applicability of the results. A Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) compliant systematic review was performed, which identified 67 MMSs describing 146 species of captive wildlife. These MMSs are becoming more common and were predominantly performed on mammals (76/146). Prospective authors are encouraged to perform MMSs on amphibians, birds, reptiles, fish, and invertebrates. The studied animals were mostly managed at institutions in the United States of America (28/67, 41.2%) and Europe (14/67, 20.9%). Classifying individuals into age groups facilitates the identification of disease trends within age classes. Only 22/67 (32.8%) studies cited justification for their age classification; classifications should be based on a referenced source on the breeding biology of the studied species. There is variation in the body systems used by authors and into which system a disease is categorized, which makes study comparisons challenging. Diseases were predominantly categorized by etiology and body system (28/77, 36.4%). Because of its ubiquity, the use of the categorization system employed by the pathology module of the Zoological Information Management System is recommended as a useful standard. This system is imperfect, and amendments to it are suggested. The results and recommendations of this study were discussed with a panel of zoo and wildlife experts; guidelines have been formulated for prospective authors aiming to conduct MMSs in captive wildlife.
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Affiliation(s)
- Kyle McCreesh
- Wildlife Health, Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire, AL9 7TA, United Kingdom,
| | - Amanda L Guthrie
- Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom
| | - Simon Spiro
- Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom
| | - Stuart Patterson
- Wildlife Health, Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire, AL9 7TA, United Kingdom
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2
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Bazzicalupo E, Lucena‐Perez M, Kleinman‐Ruiz D, Pavlov A, Trajçe A, Hoxha B, Sanaja B, Gurielidze Z, Kerdikoshvili N, Mamuchadze J, Yarovenko YA, Akkiev MI, Ratkiewicz M, Saveljev AP, Melovski D, Gavashelishvili A, Schmidt K, Godoy JA. History, demography and genetic status of Balkan and Caucasian
Lynx lynx
(Linnaeus, 1758) populations revealed by genome‐wide variation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Enrico Bazzicalupo
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | - Maria Lucena‐Perez
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | - Daniel Kleinman‐Ruiz
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
| | | | - Aleksandër Trajçe
- Protection and Preservation of Natural Environment in Albania (PPNEA) Tirana Albania
| | - Bledi Hoxha
- Protection and Preservation of Natural Environment in Albania (PPNEA) Tirana Albania
| | - Bardh Sanaja
- Environmentally Responsible Action (ERA) Peje Montenegro
| | - Zurab Gurielidze
- Program for the Ecology and Conservation of Large Mammals Institute of Ecology Ilia State University Tbilisi Georgia
| | - Niko Kerdikoshvili
- Program for the Ecology and Conservation of Large Mammals Institute of Ecology Ilia State University Tbilisi Georgia
| | | | - Yuriy A. Yarovenko
- Pre‐Caspian Institute of Biological Resources Dagestan Federal Scientific Centre of RAS Makhachkala Russian Federation
| | - Muzigit I. Akkiev
- Kabardino‐Balkarian State High‐Mountain Nature Reserve Kashkhatau Russian Federation
| | | | - Alexander P. Saveljev
- Russian Research Institute of Game Management and Fur Farming Kirov Russian Federation
| | - Dime Melovski
- Macedonian Ecological Society (MES) Skopje Macedonia
- Wildlife Sciences Georg‐August University Göttingen Germany
| | | | - Krzysztof Schmidt
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - José A. Godoy
- Department of Integrative Ecology Estación Biológica de Doñana (CSIC) Seville Spain
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3
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Lucena-Perez M, Kleinman-Ruiz D, Marmesat E, Saveljev AP, Schmidt K, Godoy JA. Bottleneck-associated changes in the genomic landscape of genetic diversity in wild lynx populations. Evol Appl 2021; 14:2664-2679. [PMID: 34815746 PMCID: PMC8591332 DOI: 10.1111/eva.13302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 01/06/2023] Open
Abstract
Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole-genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θ W diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low-frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra-conserved elements can be used as a sensitive and easy-to-apply signature of genetic erosion in wild populations.
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Affiliation(s)
- Maria Lucena-Perez
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Daniel Kleinman-Ruiz
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
- Departamento de Genética Facultad de Biología Universidad Complutense Madrid Spain
| | - Elena Marmesat
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Alexander P Saveljev
- Department of Animal Ecology Russian Research Institute of Game Management and Fur Farming Kirov Russia
| | - Krzysztof Schmidt
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - José A Godoy
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
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4
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McFarlane S, Manseau M, Wilson PJ. Spatial familial networks to infer demographic structure of wild populations. Ecol Evol 2021; 11:4507-4519. [PMID: 33976826 PMCID: PMC8093719 DOI: 10.1002/ece3.7345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 11/08/2022] Open
Abstract
In social species, reproductive success and rates of dispersal vary among individuals resulting in spatially structured populations. Network analyses of familial relationships may provide insights on how these parameters influence population-level demographic patterns. These methods, however, have rarely been applied to genetically derived pedigree data from wild populations.Here, we use parent-offspring relationships to construct familial networks from polygamous boreal woodland caribou (Rangifer tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We collected samples from 933 individuals at 15 variable microsatellite loci along with caribou-specific primers for sex identification. Using network measures, we assess the contribution of individual caribou to the population with several centrality measures and then determine which measures are best suited to inform on the population demographic structure. We investigate the centrality of individuals from eighteen different local areas, along with the entire population.We found substantial differences in centrality of individuals in different local areas, that in turn contributed differently to the full network, highlighting the importance of analyzing networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative measures to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and family cohesion across the range. We found varied levels of dispersal, fitness, and cohesion in family groups. Synthesis and applications: Our results demonstrate the value of different network measures in assessing genetically derived familial networks. The spatial application of the familial networks identified individuals presenting different fitness levels, short- and long-distance dispersing ability across the range in support of population monitoring and recovery efforts.
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Affiliation(s)
- Samantha McFarlane
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Micheline Manseau
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Paul J. Wilson
- Environmental and Life Sciences DepartmentTrent UniversityPeterboroughONCanada
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5
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Centeno-Cuadros A, Román J, Sánchez-Recuero A, Lucena-Pérez M, Delibes M, Godoy JA. Mating System, Breeding Success, and Pup Mortality of a Habitat Specialist Rodent: A Field and Molecular-based Approach. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09542-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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The rise of a large carnivore population in Central Europe: genetic evaluation of lynx reintroduction in the Harz Mountains. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01270-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractLarge carnivores have made a successful comeback across human-dominated landscapes in Central Europe. The Eurasian lynx, for instance, has been actively reintroduced in different regions. Genetic diversity is quickly eroding in these isolated, small populations, questioning the long-term success of lynx reintroductions. To track population development and genetic diversity in a reintroduced lynx population, we used microsatellite analysis and mtDNA haplotyping based on 379 samples collected during the initial 15 year period of lynx reintroduction in the Harz mountains National Park, Germany. The Harz lynx population shows higher genetic diversity relative to other lynx reintroductions, due to initial cross-breeding of divergent captive source lineages and a comparably high founder size. While the population shows significant population growth and spread into adjacent regions, genetic diversity is continiously declining. Expected heterozygosity values dropped from 0.63 after reintroduction (2006/2007) to 0.55 within a 10 year period. Despite this, the Harz lynx population is currently a viable component to an envisioned lynx metapopulation spanning across Central Europe. The ongoing genetic erosion in the Harz population along with a lack of geneflow from adjacent populations indicates that such connectivity is urgently needed to ensure long-term population persistence.
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7
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Rose C, Prange IS, Landry SM. Extirpated, immigrated, genetically stratified—first demographic assessment of a recovering bobcat (Lynx rufus) population after a century of extinction. MAMMAL RES 2020. [DOI: 10.1007/s13364-019-00462-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Reeves J, Smith C, Dierenfeld ES, Whitehouse-Tedd K. Captivity-induced metabolic programming in an endangered felid: implications for species conservation. Sci Rep 2020; 10:3630. [PMID: 32107441 PMCID: PMC7046719 DOI: 10.1038/s41598-020-60577-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/12/2020] [Indexed: 11/08/2022] Open
Abstract
Reintroduction of captive-bred individuals into the wild is an important conservation activity. However, environmental conditions can influence developmental programming, potentially causing metabolic disorders in adults. These effects are investigated here for the first time in an endangered species. Using body weight and feed intake data for Iberian lynx (Lynx pardinus) (n = 22), we compared the growth of captive versus wild born and/or reared individuals. Captive-born individuals gained weight as a function of calorie intake, unlike wild-born individuals. When compared with females reared in the wild, captive-reared females achieved a larger body size, without evidence of obesity. Captivity-associated changes to metabolic programming may compromise survival in the wild if an increased body size incurs a greater energy requirement. Large body size may also confer a competitive advantage over smaller, wild-born individuals, disrupting the social organisation of existing wild populations, and inferring long-term implications for the phenotypic composition of wild populations.
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Affiliation(s)
- Jessica Reeves
- Iberian Lynx Captive Breeding Centre "El Acebuche", Parque Nacional de Doñana, Matalascañas, 21760, Huelva, Spain
| | - Carl Smith
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, NG25 0QF, Nottinghamshire, United Kingdom
- Department of Ecology & Vertebrate Zoology, University of Łódź, 12/16 Banacha Street, 90-237, Łódź, Poland
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic
| | - Ellen S Dierenfeld
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, NG25 0QF, Nottinghamshire, United Kingdom
- Ellen S. Dierenfeld LLC, St. Louis, MO, United States of America
| | - Katherine Whitehouse-Tedd
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, NG25 0QF, Nottinghamshire, United Kingdom.
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9
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Lucena-Perez M, Marmesat E, Kleinman-Ruiz D, Martínez-Cruz B, Węcek K, Saveljev AP, Seryodkin IV, Okhlopkov I, Dvornikov MG, Ozolins J, Galsandorj N, Paunovic M, Ratkiewicz M, Schmidt K, Godoy JA. Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts. Mol Ecol 2020; 29:812-828. [PMID: 31995648 PMCID: PMC7064982 DOI: 10.1111/mec.15366] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/28/2022]
Abstract
Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Daniel Kleinman-Ruiz
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Begoña Martínez-Cruz
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Karolina Węcek
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia.,Biological Faculty of Moscow State University, Moscow, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, Vladivostok, Russia.,Far Eastern Federal University, Vladivostok, Russia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of Cryolithozone, Siberian Division of the Russian Academy of Sciences, Yakutsk, Russia
| | - Mikhail G Dvornikov
- Department of Hunting Resources, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Janis Ozolins
- Department of Hunting and Wildlife Management, Latvijas Valsts mežzinātnes institūts "Silava", Salaspils, Latvia
| | - Naranbaatar Galsandorj
- Institute of General and Experimental Biology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | | | | | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
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10
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Muranty H, Denancé C, Feugey L, Crépin JL, Barbier Y, Tartarini S, Ordidge M, Troggio M, Lateur M, Nybom H, Paprstein F, Laurens F, Durel CE. Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC PLANT BIOLOGY 2020; 20:2. [PMID: 31898487 PMCID: PMC6941274 DOI: 10.1186/s12870-019-2171-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 11/27/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. RESULTS Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. CONCLUSIONS The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.
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Affiliation(s)
- Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Laurence Feugey
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Jean-Luc Crépin
- Les Croqueurs de Pommes du Confluent Ain-Isère-Savoie, Les Avenières, France
| | - Yves Barbier
- Les Croqueurs de Pommes du Confluent Ain-Isère-Savoie, Les Avenières, France
| | - Stefano Tartarini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, UK
| | - Michela Troggio
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Gembloux, Belgium
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Balsgård, Kristianstad, Sweden
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czech Republic
| | - François Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
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11
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The use of spatially explicit capture-recapture models for estimating Iberian lynx abundance in a newly reintroduced population. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Genetic evaluation of the Iberian lynx ex situ conservation programme. Heredity (Edinb) 2019; 123:647-661. [PMID: 30952964 DOI: 10.1038/s41437-019-0217-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/09/2022] Open
Abstract
Ex situ programmes have become critical for improving the conservation of many threatened species, as they establish backup populations and provide individuals for reintroduction and reinforcement of wild populations. The Iberian lynx was considered the most threatened felid species in the world in the wake of a dramatic decline during the second half of the 20th century that reduced its numbers to around only 100 individuals. An ex situ conservation programme was established in 2003 with individuals from the two well-differentiated, remnant populations, with great success from a demographic point of view. Here, we evaluate the genetic status of the Iberian lynx captive population based on molecular data from 36 microsatellites, including patterns of relatedness and representativeness of the two remnant genetic backgrounds among founders, the evolution of diversity and inbreeding over the years, and genetic differentiation among breeding facilities. In general terms, the ex situ population harbours most of the genetic variability found in the two wild populations and has been able to maintain reasonably low levels of inbreeding and high diversity, thus validating the applied management measures and potentially representing a model for other species in need of conservation.
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13
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Proïa F, Panloup F, Trabelsi C, Clotault J. Probabilistic reconstruction of genealogies for polyploid plant species. J Theor Biol 2019; 462:537-551. [PMID: 30500601 DOI: 10.1016/j.jtbi.2018.11.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible crossbreeding patterns, our model enables us to infer and to quantify the whole potential genealogies in the population. We explain in particular how to deal with the uncertain allelic multiplicity that may occur with polyploids. Then we build an ad hoc penalized likelihood to compare genealogies and to decide whether a particular individual brings sufficient information to be included in the taken genealogy. This decision criterion enables us in a next part to suggest a greedy algorithm in order to explore missing links and to rebuild some connections in the genealogies, retrospectively. As a by-product, we also give a way to infer the individuals that may have been favored by breeders over the years. In the last part we highlight the results given by our model and our algorithm, firstly on a simulated population and then on a real population of rose bushes. Most of the methodology relies on the maximum likelihood principle and on graph theory.
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Affiliation(s)
- Frédéric Proïa
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Fabien Panloup
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Chiraz Trabelsi
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France.
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14
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Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe. Heredity (Edinb) 2018; 122:785-799. [PMID: 30470785 DOI: 10.1038/s41437-018-0167-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 11/08/2022] Open
Abstract
Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech-Slovak border. Even though the population size has been relatively stable over the period studied (2010-2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females, lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.
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González M, Gutiérrez C, Martínez R. Non-parametric Bayesian inference through MCMC method for Y-linked two-sex branching processes with blind choice. J STAT COMPUT SIM 2018. [DOI: 10.1080/00949655.2018.1526284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Miguel González
- Department of Mathematics and Instituto de Computación Científica Avanzada (ICCAEx), University of Extremadura, Badajoz, Spain
| | - Cristina Gutiérrez
- Department of Mathematics and Instituto de Computación Científica Avanzada (ICCAEx), University of Extremadura, Badajoz, Spain
| | - Rodrigo Martínez
- Department of Mathematics and Instituto de Computación Científica Avanzada (ICCAEx), University of Extremadura, Badajoz, Spain
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