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Wong W, Wang L, Schaffner SS, Li X, Cheeseman I, Anderson TJC, Vaughan A, Ferdig M, Volkman SK, Hartl DL, Wirth DF. MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603328. [PMID: 39071294 PMCID: PMC11275886 DOI: 10.1101/2024.07.12.603328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Pathogen genomics is a powerful tool for tracking infectious disease transmission. In malaria, identity-by-descent (IBD) is used to assess the genetic relatedness between parasites and has been used to study transmission and importation. In theory, IBD can be used to distinguish genealogical relationships to reconstruct transmission history or identify parasites for genotype-to-phenotype quantitative-trait-locus experiments. MalKinID (Malaria Kinship Identifier) is a new likelihood-based classification model designed to identify genealogical relationships among malaria parasites based on genome-wide IBD proportions and IBD segment distributions. MalKinID was calibrated to the genomic data from three laboratory-based genetic crosses (yielding 440 parent-child and 9060 full-sibling comparisons). MalKinID identified lab generated F1 progeny with >80% sensitivity and showed that 0.39 (95% CI 0.28, 0.49) of the second-generation progeny of a NF54 and NHP4026 cross were F1s and 0.56 (0.45, 0.67) were backcrosses of an F1 with the parental NF54 strain. In simulated outcrossed importations, MalKinID accurately reconstructs genealogy history with high precision and sensitivity, with F1-scores exceeding 0.84. However, when importation involves inbreeding, such as during serial co-transmission, the precision and sensitivity of MalKinID declined, with F1-scores of 0.76 (0.56, 0.92) and 0.23 (0.0, 0.4) for PC and FS and <0.05 for second-degree and third-degree relatives. Genealogical inference is most powered 1) when outcrossing is the norm or 2) when multi-sample comparisons based on a predefined pedigree are used. MalKinID lays the foundations for using IBD to track parasite transmission history and for separating progeny for quantitative-trait-locus experiments.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lea Wang
- Harvard College, Harvard University, Cambridge, MA, USA
| | - Stephen S Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ian Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Timothy J C Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ashley Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Michael Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- School of Nursing, Simmons University, Boston MA USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Choi YJ, Fischer K, Méité A, Koudou BG, Fischer PU, Mitreva M. Distinguishing recrudescence from reinfection in lymphatic filariasis. EBioMedicine 2024; 105:105188. [PMID: 38848649 PMCID: PMC11200287 DOI: 10.1016/j.ebiom.2024.105188] [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: 11/14/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The Global Program to Eliminate Lymphatic Filariasis (GPELF) is the largest public health program based on mass drug administration (MDA). Despite decades of MDA, ongoing transmission in some countries remains a challenge. To optimise interventions, it is critical to differentiate between recrudescence and new infections. Since adult filariae are inaccessible in humans, deriving a method that relies on the offspring microfilariae (mf) is necessary. METHODS We developed a genome amplification and kinship analysis-based approach using Brugia malayi samples from gerbils, and applied it to analyse Wuchereria bancrofti mf from humans in Côte d'Ivoire. We examined the pre-treatment genetic diversity in 269 mf collected from 18 participants, and further analysed 1-year post-treatment samples of 74 mf from 4 participants. Hemizygosity of the male X-chromosome allowed for direct inference of haplotypes, facilitating robust maternal parentage inference. To enrich parasite DNA from samples contaminated with host DNA, a whole-exome capture panel was created for W. bancrofti. FINDINGS By reconstructing and temporally tracking sibling relationships across pre- and post-treatment samples, we differentiated between new and established maternal families, suggesting reinfection in one participant and recrudescence in three participants. The estimated number of reproductively active adult females ranged between 3 and 11 in the studied participants. Population structure analysis revealed genetically distinct parasites in Côte d'Ivoire compared to samples from other countries. Exome capture identified protein-coding variants with ∼95% genotype concordance rate. INTERPRETATION We have generated resources to facilitate the development of molecular genetic tools that can estimate adult worm burdens and monitor parasite populations, thus providing essential information for the successful implementation of GPELF. FUNDING This work was financially supported by the Bill and Melinda Gates Foundation (https://www.gatesfoundation.org) under grant OPP1201530 (Co-PIs PUF & Gary J. Weil). B. malayi parasite material was generated with support of the Foundation for Barnes Jewish Hospital (PUF). In addition, the development of computational methods was supported by the National Institutes of Health under grants AI144161 (MM) and AI146353 (MM). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Young-Jun Choi
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aboulaye Méité
- Programme National de la Lutte Contre la Schistosomiase, Les Geohelminthiases et la Filariose Lymphatique, Abidjan, Côte d'Ivoire
| | - Benjamin G Koudou
- Centre Suisse de Recherche Scientifique en Côte d'Ivoire, Abidjan, Côte d'Ivoire; Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Peter U Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [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: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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5
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Rosenblatt E, Creel S, Gieder K, Murdoch J, Donovan T. Advances in wildlife abundance estimation using pedigree reconstruction. Ecol Evol 2023; 13:e10650. [PMID: 37869434 PMCID: PMC10585057 DOI: 10.1002/ece3.10650] [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: 06/05/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose (Alces americanus) population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.
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Affiliation(s)
- Elias Rosenblatt
- Vermont Cooperative Fish and Wildlife Research Unit, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
| | - Scott Creel
- Department of EcologyMontana State UniversityBozemanMontanaUSA
| | | | - James Murdoch
- Wildlife and Fisheries Biology Program, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
| | - Therese Donovan
- U.S. Geological Survey, Vermont Cooperative Fish and Wildlife Research Unit, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
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Sorum MS, Cameron MD, Crupi A, Sage GK, Talbot SL, Hilderbrand GV, Joly K. Pronounced brown bear aggregation along anadromous streams in interior Alaska. WILDLIFE BIOLOGY 2023. [DOI: 10.1002/wlb3.01057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Mathew S. Sorum
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
| | - Matthew D. Cameron
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
| | | | - George K. Sage
- Far Northwestern Inst. of Art and Science, Alaska Office Alaska USA
| | - Sandra L. Talbot
- Far Northwestern Inst. of Art and Science, Alaska Office Alaska USA
| | | | - Kyle Joly
- Gates of the Arctic National Park and Preserve, National Park Service Fairbanks Alaska USA
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7
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Wang H, Yang MA, Wangdue S, Lu H, Chen H, Li L, Dong G, Tsring T, Yuan H, He W, Ding M, Wu X, Li S, Tashi N, Yang T, Yang F, Tong Y, Chen Z, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang Z, Gao Y, Zhang M, Wang X, Zhang C, Yuan K, Ko AMS, Aldenderfer M, Gao X, Xu S, Fu Q. Human genetic history on the Tibetan Plateau in the past 5100 years. SCIENCE ADVANCES 2023; 9:eadd5582. [PMID: 36930720 PMCID: PMC10022901 DOI: 10.1126/sciadv.add5582] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Using genome-wide data of 89 ancient individuals dated to 5100 to 100 years before the present (B.P.) from 29 sites across the Tibetan Plateau, we found plateau-specific ancestry across plateau populations, with substantial genetic structure indicating high differentiation before 2500 B.P. Northeastern plateau populations rapidly showed admixture associated with millet farmers by 4700 B.P. in the Gonghe Basin. High genetic similarity on the southern and southwestern plateau showed population expansion along the Yarlung Tsangpo River since 3400 years ago. Central and southeastern plateau populations revealed extensive genetic admixture within the plateau historically, with substantial ancestry related to that found in southern and southwestern plateau populations. Over the past ~700 years, substantial gene flow from lowland East Asia further shaped the genetic landscape of present-day plateau populations. The high-altitude adaptive EPAS1 allele was found in plateau populations as early as in a 5100-year-old individual and showed a sharp increase over the past 2800 years.
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Affiliation(s)
- Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Melinda A. Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Hongliang Lu
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Haibing Yuan
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Shuai Li
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Feng Yang
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Yuanhong He
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zhaoxia Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA 95343, USA
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Qi Zhi Institute, Shanghai 200232, China
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8
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Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Bawin Y, Staelens A, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. Heredity (Edinb) 2023; 130:145-153. [PMID: 36596880 PMCID: PMC9981769 DOI: 10.1038/s41437-022-00588-0] [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: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.
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Affiliation(s)
- Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Meise Botanic Garden, Meise, Belgium.
- KU Leuven Plant Institute, Leuven, Belgium.
| | - Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium.
| | - Justin A Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ithe Mwanga Mwanga
- Centre de Recherche en Science Naturelles, Lwiro, Democratic Republic of the Congo
| | - Tshimi Ebele
- Institut National des Etudes et Recherches, Agronomique, Democratic Republic of the Congo
| | - Benoit Dhed'a
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Bawin
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Filip Vandelook
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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9
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Larroque J, Balkenhol N. A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs. PeerJ 2023; 11:e15151. [PMID: 37070094 PMCID: PMC10105560 DOI: 10.7717/peerj.15151] [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: 10/19/2022] [Accepted: 03/09/2023] [Indexed: 04/19/2023] Open
Abstract
Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).
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Affiliation(s)
- Jeremy Larroque
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| | - Niko Balkenhol
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
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10
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Euclide PT, Larson WA, Bootsma M, Miller LM, Scribner KT, Stott W, Wilson CC, Latch EK. A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus. Ecol Evol 2022; 12:e9591. [PMID: 36532137 PMCID: PMC9750844 DOI: 10.1002/ece3.9591] [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: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.
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Affiliation(s)
- Peter T. Euclide
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
| | - Wesley A. Larson
- College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA,National Marine Fisheries Service, Alaska Fisheries Science CenterNational Oceanographic and Atmospheric AdministrationJuneauAlaskaUSA
| | - Matthew Bootsma
- College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Loren M. Miller
- Minnesota Department of Natural ResourcesSt. PaulMinnesotaUSA
| | - Kim T. Scribner
- Department of Fish and WildlifeDepartment of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Wendylee Stott
- Department of Fisheries and Oceans, Artic and Aquatic Research DivisionWinnipegManitobaCanada
| | - Chris C. Wilson
- Ontario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughOntarioCanada
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWisconsinUSA
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11
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Takeuchi A, Sawayama E, Kuroki M, Miller MJ, Watanabe S, Tsukamoto K. Preliminary insight into parental contributions to Japanese eel (Anguilla japonica) preleptocephali spawned on different nights. JOURNAL OF FISH BIOLOGY 2022; 101:1601-1605. [PMID: 36097684 DOI: 10.1111/jfb.15215] [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: 05/16/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Parentage sibship-inference analyses were conducted using mtDNA sequencing and six microsatellite genotypes of 182 Japanese eel preleptocephali that were collected from one net-tow near the West Mariana Ridge in May 2014. At least 328 parents were involved in producing the 182 preleptocephali, and several parents may have spawned a few times during 3 days of a spawning period. Half-sibs suggested that a few parents mated with 1-3 partners, indicating that the Japanese eel can form spawning aggregations in which several parents mate with each other in the ocean.
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Affiliation(s)
- Aya Takeuchi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Eitaro Sawayama
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Mari Kuroki
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Michael J Miller
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shun Watanabe
- Department of Fisheries, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Katsumi Tsukamoto
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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12
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Pimid M, Krishnan KT, Ahmad AH, Mohd Naim D, Chambers GK, Mohd Nor SA, Ab Majid AH. Parentage Assignment Using Microsatellites Reveals Multiple Mating in Aedes aegypti (Diptera: Culicidae): Implications for Mating Dynamics. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1525-1533. [PMID: 35733165 DOI: 10.1093/jme/tjac081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 06/15/2023]
Abstract
The mosquito Aedes aegypti is the primary vector of the dengue, yellow fever, and chikungunya viruses. Evidence shows that Ae. aegypti males are polyandrous whereas Ae. aegypti females are monandrous in mating. However, the degree to which Ae. aegypti males and females can mate with different partners has not been rigorously tested. Therefore, this study examined the rates of polyandry via parentage assignment in three sets of competitive mating experiments using wild-type male and female Ae. aegypti. Parentage assignment was monitored using nine microsatellite DNA markers. All Ae. aegypti offspring were successfully assigned to parents with 80% or 95% confidence using CERVUS software. The results showed that both male and female Ae. aegypti mated with up to 3-4 different partners. Adults contributed differentially to the emergent offspring, with reproductive outputs ranging from 1 to 25 viable progeny. This study demonstrates a new perspective on the capabilities of male and female Ae. aegypti in mating. These findings are significant because successful deployment of reproductive control methods using genetic modification or sterile Ae. aegypti must consider the following criteria regarding their mating fitness: 1) choosing Ae. aegypti males that can mate with many different females; 2) testing how transformed Ae. aegypti male perform with polyandrous females; and 3) prioritizing the selection of polyandrous males and/or females Ae. aegypti that have the most offspring.
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Affiliation(s)
- Marcela Pimid
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600 Kelantan, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Kumara Thevan Krishnan
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600 Kelantan, Malaysia
| | - Abu Hassan Ahmad
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Darlina Mohd Naim
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Geoffrey K Chambers
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, 6140 Wellington, New Zealand
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Terengganu, Malaysia
| | - Abdul Hafiz Ab Majid
- Household & Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
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13
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Rong H, Huang B, Han X, Wu K, Xu M, Zhang W, Yang F, Xu LA. Pedigree reconstruction and genetic analysis of major ornamental characters of ornamental crabapple (Malus spp.) based on paternity analysis. Sci Rep 2022; 12:14093. [PMID: 35982151 PMCID: PMC9388634 DOI: 10.1038/s41598-022-18352-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ornamental crabapple is an important woody ornamental plant in the Northern Hemisphere. Its flowers, fruits, leaves and tree habit are all important ornamental characters. As there has been no research on the selection of superior parents and phenotypic variation, new varieties of ornamental crabapple are mainly selected from open-pollination progeny. In order to explore the transmission rule of ornamental traits between parents and offspring of crabapple, and to provide a basis for the selection of hybrid parents for directional breeding, 14 pairs of SSR markers were used in this study for paternity analysis of 384 offspring from 4 female parents crossed with 91 candidate male parents. And 273 offspring (71.1%) were matched with only the father at a 95% strict confidence level. We reconstructed 7 full-sib families (number of progeny ≥ 10) on the basis of the paternity analysis results. Genetic analysis of characters in the full-sib families revealed that green leaves and white flowers were dominant traits. All the hybrid offspring from the white flower (♀) × non-white flower (♂) cross produced white flowers, while 7.04% produced non-white flowers when both parents had white flowers. The results showed that white flowers might be a dominant qualitative trait in crabapple, while the depth of red was a quantitative trait. The genetic characteristics of green and non-green leaves and the depth of red of the peel were similar to flower color. Compared with the upright and spreading traits, the weeping trait was recessive. Some progeny showed an earlier blooming period, indicating the possibility of breeding for blooming period. Our findings are important for parent screening and improving the breeding efficiency of new varieties in ornamental crabapple hybridization.
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Affiliation(s)
- Hao Rong
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Bin Huang
- Jiangxi Provincial Key Laboratory of Camellia Germplasm Conservation and Utilization, Jiangxi Academy of Forestry, Nanchang, China
| | - Xin Han
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Kai Wu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Meng Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng Yang
- Qingdao Municipal Supervision Consulting CO., LTD, Qingdao, China
| | - Li-An Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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14
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Addis BR, Lowe WH. Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander. Am Nat 2022; 200:802-814. [DOI: 10.1086/721763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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15
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White SL, Sard NM, Brundage HM, Johnson RL, Lubinski BA, Eackles MS, Park IA, Fox DA, Kazyak DC. Evaluating sources of bias in pedigree-based estimates of breeding population size. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2602. [PMID: 35384108 DOI: 10.1002/eap.2602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Applications of genetic-based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult encounters. Estimates of breeding population size (NS ) are particularly amenable to genetic-based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of NS , is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY. We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of NS using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating NS . We applied results of the simulation analysis to evaluate N ̂ $$ \hat{N} $$ S for a population of federally endangered Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Delaware River, USA. Our results indicated that NS is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate NS and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.
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Affiliation(s)
- Shannon L White
- Akima Systems Engineers, Under Contract to the US Geological Survey, Kearneysville, West Virginia, USA
| | - Nicholas M Sard
- Department of Biological Sciences, State University of New York-Oswego, Oswego, New York, USA
| | | | - Robin L Johnson
- US Geological Survey Eastern Ecological Science Center, Kearneysville, West Virginia, USA
| | - Barbara A Lubinski
- US Geological Survey Eastern Ecological Science Center, Kearneysville, West Virginia, USA
| | - Michael S Eackles
- US Geological Survey Eastern Ecological Science Center, Kearneysville, West Virginia, USA
| | - Ian A Park
- Delaware Division of Fish and Wildlife, Dover, Delaware, USA
| | - Dewayne A Fox
- Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA
| | - David C Kazyak
- US Geological Survey Eastern Ecological Science Center, Kearneysville, West Virginia, USA
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16
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Flesch E, Graves T, Thomson J, Proffitt K, Garrott R. Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks. Ecosphere 2022. [DOI: 10.1002/ecs2.3972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Elizabeth Flesch
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
| | - Tabitha Graves
- Glacier Field Station U.S. Geological Survey West Glacier Montana USA
| | - Jennifer Thomson
- Animal and Range Sciences Department Montana State University Bozeman Montana USA
| | | | - Robert Garrott
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
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17
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A Noninvasive Genetic Insight into the Spatial and Social Organization of an Endangered Population of the Eurasian Otter (Lutra lutra, Mustelidae, Carnivora). SUSTAINABILITY 2022. [DOI: 10.3390/su14041943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The Eurasian otter is endangered in Italy, only surviving in southern river basins. The spatial and social structure of a population living at the border of the current range was explored through a noninvasive genetic study along 174 km of the Sangro river. Sampling was conducted in 2011 and 2012, collecting spraints and anal jellies at 62 marking sites. Samples were successfully genotyped at 13 nuclear microsatellites and the ZFX/ZFY locus for molecular sexing, resulting in 14 distinct genotypes (4 females, 2 possible females, 8 males), from 35 marking sites. Mean captures/recaptures rate was 3.8 captures/individual, with males being recaptured more frequently than females. Spatial overlap among individuals was analyzed through a linear regression model fitted against sibship categories and sex pairing. Nine out of the fourteen genotyped individuals belonged to three full-sib clusters, while five individuals had no full-sibs in the population. Full-sibs overlapped more than half-sibs, while male–male pairs showed significantly higher spatial overlap than both male–female and female–female pairs. Estimated mean density was 0.152 otters/km and 2.4 individuals/10 × 10 km grid cell. Accordingly, the 3440 grid cells of otter occurrence in Italy could likely host about 8000 otters, suggesting the current population has become larger than the minimum viable population size.
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18
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Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population. FORESTS 2022. [DOI: 10.3390/f13020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak.
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19
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Rueda D, Awika HO, Bedre R, Kandel DR, Mandadi KK, Crosby K, Avila CA. Phenotypic Diversity and Association Mapping of Ascorbic Acid Content in Spinach. Front Genet 2022; 12:752313. [PMID: 35046997 PMCID: PMC8762172 DOI: 10.3389/fgene.2021.752313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/15/2021] [Indexed: 11/23/2022] Open
Abstract
Ascorbic acid (AsA), or vitamin C, is an essential nutrient for humans. In plants, AsA functions as an antioxidant during normal metabolism or in response to stress. Spinach is a highly nutritious green leafy vegetable that is consumed fresh, cooked or as a part of other dishes. One current goal in spinach breeding programs is to enhance quality and nutritional content. However, little is known about the diversity of nutritional content present in spinach germplasm, especially for AsA content. In this study, a worldwide panel of 352 accessions was screened for AsA content showing that variability in spinach germplasm is high and could be utilized for cultivar improvement. In addition, a genome-wide association study for marker-trait association was performed using three models, and associated markers were searched in the genome for functional annotation analysis. The generalized linear model (GLM), the compressed mixed linear model (CMLM) based on population parameters previously determined (P3D) and the perMarker model together identified a total of 490 significant markers distributed across all six spinach chromosomes indicating the complex inheritance of the trait. The different association models identified unique and overlapping marker sets, where 27 markers were identified by all three models. Identified high AsA content accessions can be used as parental lines for trait introgression and to create segregating populations for further genetic analysis. Bioinformatic analysis indicated that identified markers can differentiate between high and low AsA content accessions and that, upon validation, these markers should be useful for breeding programs.
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Affiliation(s)
- Dario Rueda
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Henry O Awika
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Devi R Kandel
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States.,Department of Plant Pathology and Microbiology, College Station, TX, United States
| | - Kevin Crosby
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Carlos A Avila
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States.,Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
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20
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Poommouang A, Piboon P, Buddhachat K, Brown JL, Kriangwanich W, Chomdej S, Kampuansai J, Mekchay S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Microsatellite Polymorphism and the Population Structure of Dugongs (Dugong dugon) in Thailand. Animals (Basel) 2022; 12:ani12030235. [PMID: 35158560 PMCID: PMC8833502 DOI: 10.3390/ani12030235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary For this study, skin samples were analyzed from 77 individual stranded dugongs collected in Thai waters from 1994–2019 using six microsatellite markers to assess the genetic diversity and population structure. Dugongs in the Andaman Sea had higher genetic variation than those in the Gulf of Thailand. Populations in Trang, Satun and some areas of Krabi had highest diversity compared to other regions of Thailand. The analysis of Bayesian genetic clustering showed that dugongs in Thailand consist of five genetic groups. Furthermore, dugongs in the middle and lower Andaman Sea presented the greatest gene flow compared to other regions. Based on calculation of inbreeding coefficients, dugong populations in the Sea of Thailand are experiencing some levels of inbreeding, and so may warrant special protections. Results of this study provide important information on genetic diversity and genetic population structuring of dugongs in Thailand and for understanding the genetic status of dugongs that can lead to improved management and conservation of this endangered species. Abstract The dugong (Dugong dugon) is an endangered species of marine mammals, so knowledge of genetic diversity of these populations is important for conservation planning within different habitats. In this study, six microsatellite markers were used to assess the genetic diversity and population structure of 77 dugongs from skin samples of stranded animals collected from 1994–2019 (69 from Andaman Sea and 8 from the Gulf of Thailand). Our results found that dugongs in the Andaman Sea had higher genetic variation than those in the Gulf of Thailand. Populations in Trang, Satun, and some areas of Krabi had highest diversity compared to other regions of Thailand. Bayesian genetic clustering analysis revealed that dugongs in Thailand consist of five genetic groups. Moreover, dugongs in the middle and lower Andaman Sea presented the greatest gene flow compared to other regions. However, based on calculation of inbreeding coefficients (Fis value = 0.239), dugong populations in the Sea of Thailand are experiencing some levels of inbreeding, and so may warrant special protections. These results provide important information for understanding the genetic status of dugongs that can lead to improved management and conservation of this endangered species.
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Affiliation(s)
- Anocha Poommouang
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Promporn Piboon
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Janine L. Brown
- Smithsonian Conservation Biology Institute, Center for Species Survival, 1500 Remount Road, Front Royal, VA 22630, USA;
| | - Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | | | | | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (A.P.); (P.P.); (W.K.)
- Excellence Center in Veterinary Bioscience, Chiang Mai 50100, Thailand; (K.B.); (S.C.)
- Correspondence: ; Tel.: +66-53-948046
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21
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Ekanayake-Weber M, Swedell L. An agent-based model of coercive female transfer in a multilevel society. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Teixeira H, Salmona J, Arredondo A, Mourato B, Manzi S, Rakotondravony R, Mazet O, Chikhi L, Metzger J, Radespiel U. Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar. BMC Ecol Evol 2021; 21:197. [PMID: 34727890 PMCID: PMC8561976 DOI: 10.1186/s12862-021-01929-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets. RESULTS We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus. CONCLUSION Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.
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Affiliation(s)
- Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Armando Arredondo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Beatriz Mourato
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Sophie Manzi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
| | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559, Hannover, Germany
- Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
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Dickel L, Arcese P, Nietlisbach P, Keller LF, Jensen H, Reid JM. Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation. Mol Ecol 2021; 30:5674-5686. [PMID: 34516687 DOI: 10.1111/mec.16173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
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Affiliation(s)
- Lisa Dickel
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jane M Reid
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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24
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de Deus ARS, Silva GR, Sena LS, Britto FB, de Carvalho DA, de Freitas JVG, Sarmento JLR. Comparison of kinship estimates in Santa Inês sheep using microsatellite and genome-wide SNP markers. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Meta-analytic evidence that animals rarely avoid inbreeding. Nat Ecol Evol 2021; 5:949-964. [PMID: 33941905 DOI: 10.1038/s41559-021-01453-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Animals are usually expected to avoid mating with relatives (kin avoidance) as incestuous mating can lead to the expression of inbreeding depression. Yet, theoretical models predict that unbiased mating with regards to kinship should be common, and that under some conditions, the inclusive fitness benefits associated with inbreeding can even lead to a preference for mating with kin. This mismatch between empirical and theoretical expectations generates uncertainty as to the prevalence of inbreeding avoidance in animals. Here, we synthesized 677 effect sizes from 139 experimental studies of mate choice for kin versus non-kin in diploid animals, representing 40 years of research, using a meta-analytical approach. Our meta-analysis revealed little support for the widely held view that animals avoid mating with kin, despite clear evidence of publication bias. Instead, unbiased mating with regards to kinship appears widespread across animals and experimental conditions. The significance of a variety of moderators was explored using meta-regressions, revealing that the degree of relatedness and prior experience with kin explained some variation in the effect sizes. Yet, we found no difference in kin avoidance between males and females, choice and no-choice experiments, mated and virgin animals or between humans and animals. Our findings highlight the need to rethink the widely held view that inbreeding avoidance is a given in experimental studies.
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26
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Ding J, Dimitriadou E, Tšuiko O, Destouni A, Melotte C, Van Den Bogaert K, Debrock S, Jatsenko T, Esteki MZ, Voet T, Peeraer K, Denayer E, Vermeesch JR. Identity-by-state-based haplotyping expands the application of comprehensive preimplantation genetic testing. Hum Reprod 2021; 35:718-726. [PMID: 32198505 DOI: 10.1093/humrep/dez285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION Is it possible to haplotype parents using parental siblings to leverage preimplantation genetic testing (PGT) for monogenic diseases and aneuploidy (comprehensive PGT) by genome-wide haplotyping? SUMMARY ANSWER We imputed identity-by-state (IBS) sharing of parental siblings to phase parental genotypes. WHAT IS KNOWN ALREADY Genome-wide haplotyping of preimplantation embryos is being implemented as a generic approach for genetic diagnosis of inherited single-gene disorders. To enable the phasing of genotypes into haplotypes, genotyping the direct family members of the prospective parent carrying the mutation is required. Current approaches require genotypes of either (i) both or one of the parents of the affected prospective parent or (ii) an affected or an unaffected child of the couple. However, this approach cannot be used when parents or children are not attainable, prompting an investigation into alternative phasing options. STUDY DESIGN, SIZE, DURATION This is a retrospective validation study, which applied IBS-based phasing of parental haplotypes in 56 embryos derived from 12 PGT families. Genome-wide haplotypes and copy number profiles generated for each embryo using the new phasing approach were compared with the reference PGT method to evaluate the diagnostic concordance. PARTICIPANTS/MATERIALS, SETTING, METHODS This study included 12 couples with a known hereditary genetic disorder, participating in the comprehensive PGT program and with at least one parental sibling available (e.g. brother and/or sister). Genotyping data from both prospective parents and the parental sibling(s) were used to perform IBS-based phasing and to trace the disease-associated alleles. The outcome of the IBS-based PGT was compared with the results of the clinically implemented reference haplotyping-based PGT method. MAIN RESULTS AND THE ROLE OF CHANCE IBS-based haplotyping was performed for 12 PGT families. In accordance with the theoretical prediction of allele sharing between sibling pairs, 6 out of 12 (50%) couples or 23 out of 56 embryos could be phased using parental siblings. In families where phasing was possible, haplotype calling in the locus of interest was 100% concordant between the reference PGT method and IBS-based approach using parental siblings. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Phasing of parental haplotypes will only be possible when the disease locus lies in an informative region (categorized as IBS1). Phasing prospective parents using relatives with reduced genetic relatedness as a reference (e.g. siblings) decreases the size and the occurrence of informative IBS1 regions, necessary for haplotype calling. By including more than one extended family member, the chance of obtaining IBS1 coverage in the interrogated locus can be increased. A pre-PGT work-up can define whether the carrier couple could benefit from this approach. WIDER IMPLICATIONS OF THE FINDINGS Phasing by relatives extends the potential of comprehensive PGT, since it allows the inclusion of couples who do not have access to the standard phasing references, such as parents or offspring. STUDY FUNDING/COMPETING INTEREST(S) The study was funded by the KU Leuven grant (C14/18/092), Research Foundation Flanders (FWO; GA09311N), Horizon 2020 innovation programme (WIDENLIFE, 692065) and Agilent Technologies. J.R.V., T.V. and M.Z.E. are co-inventors of a patent ZL910050-PCT/EP2011/060211-WO/2011/157846 'Methods for haplotyping single-cells' and ZL913096-PCT/EP2014/068315-WO/2015/028576 'Haplotyping and copy number typing using polymorphic variant allelic frequencies' licensed to Agilent Technologies. The other authors have no conflict of interest to declare.
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Affiliation(s)
- Jia Ding
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Eftychia Dimitriadou
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Olga Tšuiko
- Laboratory of Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Aspasia Destouni
- Laboratory of Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA.,Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA 70803, USA
| | - Cindy Melotte
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Kris Van Den Bogaert
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven 3000, Belgium
| | - Tatjana Jatsenko
- Laboratory of Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Masoud Zamani Esteki
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht 6229 HX, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven 3000, Belgium
| | - Ellen Denayer
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium.,Laboratory of Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, Leuven 3000, Belgium
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Sarano F, Girardet J, Sarano V, Vitry H, Preud'homme A, Heuzey R, Garcia-Cegarra AM, Madon B, Delfour F, Glotin H, Adam O, Jung JL. Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201794. [PMID: 33972866 PMCID: PMC8074673 DOI: 10.1098/rsos.201794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.
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Affiliation(s)
| | - Justine Girardet
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
| | | | - Hugues Vitry
- Marine Megafauna Conservation Organisation, Mauritius
| | | | | | - Ana M. Garcia-Cegarra
- Centro de Investigación de Fauna Marina y Avistamiento de Cetáceos, CIFAMAC, Mejillones, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Antofagasta, Chile
| | - Bénédicte Madon
- Université de Brest, AMURE - Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer, Plouzané, France
| | - Fabienne Delfour
- Laboratoire d'Ethologie Expérimentale et Comparée EA 4443, Université Paris 13, Sorbonne Paris Cité, Villetaneuse, France
| | - Hervé Glotin
- Toulon University, Aix Marseille Université, CNRS, LIS, DYNI Team, Marseille, France
| | - Olivier Adam
- Sorbonne Université, CNRS, Institut Jean Le Rond d'Alembert, UMR 7190, Paris, France
- Institute of Neurosciences Paris-Saclay, Bioacoustics Team, CNRS UMR 9197, Université Paris Sud, Orsay, France
| | - Jean-Luc Jung
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
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28
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Huang K, Huber G, Ritland K, Dunn DW, Li B. Performing parentage analysis for polysomic inheritances based on allelic phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6080682. [PMID: 33585871 PMCID: PMC8022955 DOI: 10.1093/g3journal/jkaa064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Polyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (1) double-reduction, (2) null alleles, (3) negative amplification, (4) genotyping errors and (5) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the genotyping error rate and the sample rate. We make our new methods freely available in the software package polygene, at http://github.com/huangkang1987/polygene.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Gwendolyn Huber
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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Karamanlidis AA, Kopatz A, de Gabriel Hernando M. Dispersal patterns of a recovering brown bear (Ursus arctos) population in a human-dominated landscape. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Despite increasing habitat fragmentation, large carnivore populations in parts of Europe have been recovering and expanding into human-dominated areas. Knowledge of animal dispersal patterns in such areas is important for their conservation, management, and coexistence with humans. We used genetic data based on 15 microsatellite markers from 312 individuals (98 females, 214 males) to assess kinship and dispersal patterns during the recovery and spatial expansion of a wild brown bear (Ursus arctos) population (2003–2010) in the human-dominated landscape of Greece. We hypothesized that bear dispersal in Greece was sex-biased, with females being more philopatric and males dispersing more frequently and over greater distances. Dispersal indeed was sex-biased, with males dispersing more frequently and farther than females. Overall, females were found to be philopatric; males also appeared to be philopatric, but to a lesser degree. However, a high proportion of females displayed dispersal behavior, which may be indicative of a pre-saturation stage of the population in that part of the country. Our results indicate that dispersal may be due to evading competition and avoiding inbreeding. We also documented long-distance dispersal of bears, which is considered to be indicative of a spatially expanding population. Our results highlight the value of using noninvasive genetic monitoring data to assess kinship among individuals and study dispersal patterns in human-dominated landscapes. Brown bears remain threatened in Greece; we therefore recommend systematic genetic monitoring of the species in combination with careful habitat management to protect suitable habitat (i.e., dispersal corridors) and ultimately ensure co-existence with humans and survival of brown bears in the country.
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Affiliation(s)
- Alexandros A Karamanlidis
- ARCTUROS, Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, Florina, Greece
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander Kopatz
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Miguel de Gabriel Hernando
- ARCTUROS, Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, Florina, Greece
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, Universidad de León, León, Spain
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30
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Levasseur KE, Stapleton SP, Quattro JM. Precise natal homing and an estimate of age at sexual maturity in hawksbill turtles. Anim Conserv 2020. [DOI: 10.1111/acv.12657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- K. E. Levasseur
- Department of Biological Sciences University of South Carolina Columbia SC USA
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
| | - S. P. Stapleton
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
- Department of Fisheries, Wildlife and Conservation Biology University of Minnesota St. Paul MN USA
| | - J. M. Quattro
- Department of Biological Sciences University of South Carolina Columbia SC USA
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31
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Evidence for Nest-Site Fidelity but Not Natal Homing in Bog Turtles (Glyptemys muhlenbergii). J HERPETOL 2020. [DOI: 10.1670/19-073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Rabier R, Robert A, Lacroix F, Lesobre L. Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses. Zoo Biol 2020; 39:422-435. [PMID: 32956518 DOI: 10.1002/zoo.21569] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Protection and restoration of species in the wild may require conservation breeding programs under genetic management to minimize deleterious effects of genetic changes that occur in captivity, while preserving populations' genetic diversity and evolutionary resilience. Here, through interannual pedigree analyses, we first assessed the efficiency of a 21-year genetic management, including minimization of mean kinship, inbreeding avoidance, and regular addition of founders, of a conservation breeding program targeting on Houbara bustard (Chlamydotis undulata undulata) in Morocco. Secondly, we compared pedigree analyses, the classical way of assessing and managing genetic diversity in captivity, to molecular analyses based on seven microsatellites. Pedigree-based results indicated an efficient maintenance of the genetic diversity (99% of the initial genetic diversity retained) while molecular-based results indicated an increase in allelic richness and an increase in unbiased expected heterozygosity across time. The pedigree-based average inbreeding coefficient F remained low (between 0.0004 and 0.003 in 2017) while the proportion of highly inbred individuals (F > .1) decreased over time and reached 0.2% in 2017. Furthermore, pedigree-based F and molecular-based individual multilocus heterozygosity were weakly negatively correlated, (Pearson's r = -.061 when considering all genotyped individuals), suggesting that they cannot be considered as alternatives, but rather as complementary sources of information. These findings suggest that a strict genetic monitoring and management, based on both pedigree and molecular tools can help mitigate genetic changes and allow to preserve genetic diversity and evolutionary resilience in conservation breeding programs.
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Affiliation(s)
- Robin Rabier
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France.,Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Alexandre Robert
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France
| | - Frédéric Lacroix
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Loïc Lesobre
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
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Ching-Min Sun N, Chang SP, Lin JS, Tseng YW, Jai-Chyi Pei K, Hung KH. The genetic structure and mating system of a recovered Chinese pangolin population (Manis pentadactyla Linnaeus, 1758) as inferred by microsatellite markers. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution. Genes (Basel) 2020; 11:genes11080945. [PMID: 32824315 PMCID: PMC7464534 DOI: 10.3390/genes11080945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.
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Silver‐Gorges I, Koval J, Rodriguez‐Zarate CJ, Paladino FV, Jordan M. Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific Olive ridley sea turtles ( Lepidochelys olivacea). Ecol Evol 2020; 10:8688-8704. [PMID: 32884651 PMCID: PMC7452818 DOI: 10.1002/ece3.6564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 12/29/2022] Open
Abstract
Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial control region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (F ST = 0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and preexisting microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (F ST = 0.08, p < .001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (F ST = 0.103, p < .001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p < .001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life history, particularly in light of the natal-homing paradigm.
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Affiliation(s)
- Ian Silver‐Gorges
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Julianne Koval
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Clara J. Rodriguez‐Zarate
- Marine Turtle Conservation ProgrammeEmirates Nature in Association with World Wide Fund for Nature (WWF)DubaiUnited Arab Emirates
| | - Frank V. Paladino
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Mark Jordan
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
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From molecules to populations: appreciating and estimating recombination rate variation. Nat Rev Genet 2020; 21:476-492. [DOI: 10.1038/s41576-020-0240-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 02/07/2023]
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Barros J, Winkler FM, Velasco LA. Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles. Ecol Evol 2020; 10:3919-3931. [PMID: 32489620 PMCID: PMC7244797 DOI: 10.1002/ece3.6080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H-W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.
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Affiliation(s)
- Judith Barros
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
| | - Federico M. Winkler
- Departamento de Biología MarinaFacultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
- Centro de Innovación Acuícola AquaPacíficoCoquimboChile
- Centro de Estudios Avanzados en Zona Áridas (CEAZA)CoquimboChile
| | - Luz Adriana Velasco
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
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Douglas MR, Anthonysamy WJB, Mussmann SM, Davis MA, Louis W, Douglas ME. Multi-targeted management of upland game birds at the agroecosystem interface in midwestern North America. PLoS One 2020; 15:e0230735. [PMID: 32339176 PMCID: PMC7185590 DOI: 10.1371/journal.pone.0230735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/06/2020] [Indexed: 11/18/2022] Open
Abstract
Despite its imperative, biodiversity conservation is chronically underfunded, a deficiency that often forces management agencies to prioritize. Single-species recovery thus becomes a focus (often with socio-political implications), whereas a more economical approach would be the transition to multi-targeted management (= MTM). This challenge is best represented in Midwestern North America where biodiversity has been impacted by 300+ years of chronic anthropogenic disturbance such that native tall-grass prairie is now supplanted by an agroecosystem. Here, we develop an MTM with a population genetic metric to collaboratively manage three Illinois upland gamebirds: common pheasant (Phasianus colchicus; pheasant), northern bobwhite quail (Colinus virginianus; quail), and threatened-endangered (T&E) greater prairie chicken (Tympanuchus cupido pinnatus; prairie chicken). We first genotyped our study pheasant at 19 microsatellite DNA loci and identified three captive breeding stocks (N = 143; IL Department of Natural Resources) as being significantly bottlenecked, with relatedness >1st-cousin (μR = 0.158). 'Wild' (non-stocked) pheasant [N = 543; 14 Pheasant-Habitat-Areas (PHAs)] were also bottlenecked, significantly interrelated (μR = 0.150) and differentiated (μFST = 0.047), yet distinct from propagation stock. PHAs that encompassed significantly with larger areas also reflected greater effective population sizes (μNE = 43; P<0.007). We juxtaposed these data against previously published results for prairie chicken and quail, and found population genetic structure driven by drift, habitat/climate impacts, and gender-biased selection via hunter-harvest. Each species (hunter-harvested or T&E) is independently managed, yet their composite population genetic baseline provides the quantitative criteria needed for an upland game bird MTM. Its implementation would require agricultural plots to be rehabilitated/reclaimed using a land-sharing/sparing portfolio that differs markedly from the Conservation Reserve Program (CRP), where sequestered land decreases as agricultural prices escalate. Cost-savings for an MTM would accrue by synchronizing single-species management with a dwindling hunter-harvest program, and by eliminating propagation/stocking programs. This would sustain not only native grasslands and their resident species, but also accelerate conservation at the wildlife-agroecosystem interface.
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Affiliation(s)
- Marlis R. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | | | - Steven M. Mussmann
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Mark A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Wade Louis
- Illinois Department of Natural Resources, Gibson City, Illinois, United States of America
| | - Michael E. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
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Naude VN, Balme GA, O'Riain J, Hunter LT, Fattebert J, Dickerson T, Bishop JM. Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards. Ecol Evol 2020; 10:3605-3619. [PMID: 32313621 PMCID: PMC7160178 DOI: 10.1002/ece3.6089] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 11/07/2022] Open
Abstract
Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home-ranges) could disrupt natal dispersal mechanisms, with long-term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male-biased natal dispersal. Using a combination of spatial (home-range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin-clustering in males of this historically exploited population is comparable to that of females in a well-protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.
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Affiliation(s)
- Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
- PantheraNew YorkNYUSA
| | | | - Justin O'Riain
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Luke T.B. Hunter
- Wildlife Conservation SocietyBronxNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julien Fattebert
- PantheraNew YorkNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
- Wyoming Cooperative Fish and Wildlife Research UnitDepartment of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
| | | | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
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Bachorec E, Horáček I, Hulva P, Konečný A, Lučan RK, Jedlička P, Shohdi WM, Řeřucha Š, Abi-Said M, Bartonička T. Spatial networks differ when food supply changes: Foraging strategy of Egyptian fruit bats. PLoS One 2020; 15:e0229110. [PMID: 32097434 PMCID: PMC7041839 DOI: 10.1371/journal.pone.0229110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
Animals are faced with a range of ecological constraints that shape their behavioural decisions. Habitat features that affect resource abundance will also have an impact, especially as regards spatial distribution, which will in turn affect associations between the animals. Here we utilised a network approach, using spatial and genetic data, to describe patterns in use of space (foraging sites) by free-ranging Egyptian fruit bats (Rousettus aegyptiacus) at the Dakhla Oasis in Egypt. We observed a decrease in home range size during spring, when food availability was lowest, which was reflected by differences in space sharing networks. Our data showed that when food was abundant, space sharing networks were less connected and more related individuals shared more foraging sites. In comparison, when food was scarce the bats had few possibilities to decide where and with whom to forage. Overall, both networks had high mean degree, suggesting communal knowledge of predictable food distribution.
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Affiliation(s)
- Erik Bachorec
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Ivan Horáček
- Department of Zoology, Charles University in Prague, Viničná, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Viničná, Prague, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Radek K. Lučan
- Department of Zoology, Charles University in Prague, Viničná, Prague, Czech Republic
| | - Petr Jedlička
- Institute of Scientific Instruments of the Czech Academy of Sciences (ISI), Královopolská, Brno, Czech Republic
| | | | - Šimon Řeřucha
- Institute of Scientific Instruments of the Czech Academy of Sciences (ISI), Královopolská, Brno, Czech Republic
| | - Mounir Abi-Said
- Department of Earth and Life Sciences, Faculty of Sciences II, Lebanese University, Fanar, Lebanon
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
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Sard NM, Smith SR, Homola JJ, Kanefsky J, Bravener G, Adams JV, Holbrook CM, Hrodey PJ, Tallon K, Scribner KT. RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecol Evol 2020; 10:1469-1488. [PMID: 32076528 PMCID: PMC7029094 DOI: 10.1002/ece3.6001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.
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Affiliation(s)
- Nicholas M. Sard
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Biology DepartmentSUNY OswegoOswegoNew York
| | - Seth R. Smith
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jeannette Kanefsky
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | | | - Jean V. Adams
- Great Lakes Science CenterU.S. Geological SurveyAnn ArborMichigan
| | - Christopher M. Holbrook
- Great Lakes Science CenterHammond Bay Biological StationU.S. Geological SurveyMillersburgMichigan
| | | | - Kevin Tallon
- Fisheries and Oceans CanadaSault Ste. MarieONCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Department of Integrative BiologyState UniversityEast LansingMichigan
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Waters CD, Hard JJ, Fast DE, Knudsen CM, Bosch WJ, Naish KA. Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon. Mol Ecol 2020; 29:658-672. [PMID: 31957935 DOI: 10.1111/mec.15356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023]
Abstract
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jeffrey J Hard
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | | | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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Ishizuka S, Takemoto H, Sakamaki T, Tokuyama N, Toda K, Hashimoto C, Furuichi T. Comparisons of between-group differentiation in male kinship between bonobos and chimpanzees. Sci Rep 2020; 10:251. [PMID: 31937864 PMCID: PMC6959343 DOI: 10.1038/s41598-019-57133-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Patterns of kinship among individuals in different groups have been rarely examined in animals. Two closest living relatives of humans, bonobos and chimpanzees share many characteristics of social systems including male philopatry, whereas one major difference between the two species is the nature of intergroup relationship. Intergroup relationship is basically antagonistic and males sometimes kill individuals of other groups in chimpanzees, whereas it is much more moderate in bonobos and copulations between individuals of different groups are often observed during intergroup encounters. Such behavioural differences may facilitate more frequent between-group male gene flow and greater between-group differentiation in male kinship in bonobos than in chimpanzees. Here we compared differences between average relatedness among males within groups and that among males of neighbouring groups, and between-group male genetic distance between bonobos and chimpanzees. Contrary to expectation, the differences between average relatedness among males within groups and that among males of neighbouring groups were significantly greater in bonobos than in chimpanzees. There were no significant differences in autosomal and Y-chromosomal between-group male genetic distance between the two species. Our results showed that intergroup male kinship is similarly or more differentiated in bonobos than in chimpanzees.
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Affiliation(s)
- Shintaro Ishizuka
- Primate Research Institute, Kyoto University, Inuyama, Japan.
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan.
| | | | - Tetsuya Sakamaki
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Antwerp Zoo Foundation, Antwerp, Belgium
| | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Yokosuka, Japan
| | - Kazuya Toda
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Chie Hashimoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
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Koch K, Pink C, Hamilton N, Algar D. A population genetic study of feral cats on Christmas Island. AUST J ZOOL 2020. [DOI: 10.1071/zo20081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Feral and stray cats are a major threat for endemic species on Christmas Island and have been contributing to their decline. Cats were introduced to Christmas Island in 1888 and are now distributed across the whole island. We analysed the genetic population structure and diversity of feral and stray cats on Christmas Island to evaluate connectivity across the island and the possibility of discernible populations that could be targeted separately. Results indicate no differentiated population structure across the island, with cats facing no habitat obstacles to reduce their dispersal abilities across the island. We found high kin structure, suggesting individuals breeding successfully on the whole island. With the management of domestic and feral/stray cats since 2010, removal efforts targeting the whole island have successfully reduced the effective population size of feral/stray cats in the last five years. We suggest the use of various management techniques to facilitate future removal efforts, especially in areas on the island that are difficult to access.
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45
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Awika HO, Marconi TG, Bedre R, Mandadi KK, Avila CA. Minor alleles are associated with white rust ( Albugo occidentalis) susceptibility in spinach ( Spinacia oleracea). HORTICULTURE RESEARCH 2019; 6:129. [PMID: 31814982 PMCID: PMC6885047 DOI: 10.1038/s41438-019-0214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/29/2019] [Accepted: 11/03/2019] [Indexed: 05/05/2023]
Abstract
Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.
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Affiliation(s)
- Henry O. Awika
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Thiago G. Marconi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Plant Pathology and Microbiology, College Station, TX 77843 USA
| | - Carlos A. Avila
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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Burgess SC, Sander L, Bueno M. How relatedness between mates influences reproductive success: An experimental analysis of self-fertilization and biparental inbreeding in a marine bryozoan. Ecol Evol 2019; 9:11353-11366. [PMID: 31641478 PMCID: PMC6802076 DOI: 10.1002/ece3.5636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 11/21/2022] Open
Abstract
Kin associations increase the potential for inbreeding. The potential for inbreeding does not, however, make inbreeding inevitable. Numerous factors influence whether inbreeding preference, avoidance, or tolerance evolves, and, in hermaphrodites where both self-fertilization and biparental inbreeding are possible, it remains particularly difficult to predict how selection acts on the overall inbreeding strategy, and to distinguish the type of inbreeding when making inferences from genetic markers. Therefore, we undertook an empirical analysis on an understudied type of mating system (spermcast mating in the marine bryozoan, Bugula neritina) that provides numerous opportunities for inbreeding preference, avoidance, and tolerance. We created experimental crosses, containing three generations from two populations to estimate how parental reproductive success varies across parental relatedness, ranging from self, siblings, and nonsiblings from within the same population. We found that the production of viable selfed offspring was extremely rare (only one colony produced three selfed offspring) and biparental inbreeding more common. Paternity analysis using 16 microsatellite markers confirmed outcrossing. The production of juveniles was lower for sib mating compared with nonsib mating. We found little evidence for consistent inbreeding, in terms of nonrandom mating, in adult samples collected from three populations, using multiple population genetic inferences. Our results suggest several testable hypotheses that potentially explain the overall mating and dispersal strategy in this species, including early inbreeding depression, inbreeding avoidance through cryptic mate choice, and differential dispersal distances of sperm and larvae.
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Affiliation(s)
- Scott C. Burgess
- Department of Biological ScienceFlorida State UniversityTallahasseeFLUSA
| | - Lisa Sander
- Department of Biological ScienceFlorida State UniversityTallahasseeFLUSA
| | - Marília Bueno
- Department of Biological ScienceFlorida State UniversityTallahasseeFLUSA
- Present address:
Departamento de Biologia AnimalInstituto de BiologiaUniversidade Estadual de Campinas – UNICAMPCampinasBrazil
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Lee SM, Moon HC, Jeon HS, Song EG, Woo D, An J, Lee MY. A core set of microsatellite loci for yellow-throated marten, Martes flavigula: a case of inferences of family relationships. Genes Genomics 2019; 41:1457-1465. [PMID: 31541356 DOI: 10.1007/s13258-019-00869-9] [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: 03/18/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Microsatellite markers are an ideal molecular marker for population genetic studies such as population structure, pedigree, and kinship. The yellow-throated marten (Martes flavigula) is widely distributed in coniferous and deciduous forests of eastern Asia and plays the role of an indicator and umbrella species in South Korea, given the absence of top predators such as tiger and leopard. OBJECTIVE The aim of our study was to establish a core set of microsatellite markers that could be used for a population genetics study on M. flavigula. METHODS We characterized 21 di-motif microsatellites for M. flavigula by Illumina next-generation sequencing. We evaluated them for a population genetics study against five established criteria together with 33 previously developed microsatellites. We calculated relatedness values between individual yellow-throated martens in two groups that were suspected to be siblings using the selected core set of markers to confirm applicability. RESULTS Twenty-three loci were determined as the core set of microsatellite markers. The probability of identity P(ID) and probability of identity between siblings P(ID)sib of the core set was estimated as 2-15 and 2.2-7, respectively. Relatedness values between individuals in the two groups of M. flavigula revealed that one of the pairs was sisters, confirming that the core set can be applied to kinship studies. CONCLUSION The developed microsatellite core set in this study is expected to contribute to studies on molecular ecology and population structure of M. flavigula.
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Affiliation(s)
- Seon-Mi Lee
- Animal Resources Division, National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Hea Chang Moon
- Kookmin University, 77 Jeongneung-ro, Seongbuk-Gu, Seoul, 02707, Republic of Korea
| | - Hye Sook Jeon
- Animal Resources Division, National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Eui-Geun Song
- National Institute of Ecology, 1210 Geumgang-ro, Seocheon, Chungcheongnam-do, 33657, Republic of Korea
| | - Donggul Woo
- National Institute of Ecology, 1210 Geumgang-ro, Seocheon, Chungcheongnam-do, 33657, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Mu-Yeong Lee
- DNA Analysis Division, Seoul Institute, National Forensic Service, Seoul, 08636, Republic of Korea.
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Ko A, Nielsen R. Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo. Genetics 2019; 212:855-868. [PMID: 31123041 PMCID: PMC6614905 DOI: 10.1534/genetics.119.302280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/16/2019] [Indexed: 12/31/2022] Open
Abstract
Pedigrees provide the genealogical relationships among individuals at a fine resolution and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of the short-term effective population size [Formula: see text], which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and [Formula: see text] from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals within a single generation with the use of a composite likelihood, which significantly increases computational efficiency. We show, on simulated data, that our method is able to jointly estimate relationships up to first cousins and [Formula: see text] with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.
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Affiliation(s)
- Amy Ko
- Department of Integrative Biology, University of California, Berkeley, 94720 California
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, 94720 California
- Department of Statistics, University of California, Berkeley, 94720 California
- Museum of Natural History, University of Copenhagen, 1123 Denmark
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Roques S, Chancerel E, Boury C, Pierre M, Acolas M. From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon. Ecol Evol 2019; 9:7017-7029. [PMID: 31380030 PMCID: PMC6662312 DOI: 10.1002/ece3.5268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/12/2019] [Accepted: 04/04/2019] [Indexed: 01/06/2023] Open
Abstract
The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.
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Affiliation(s)
- Séverine Roques
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
| | | | | | - Maud Pierre
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
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