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Pan H, Deng L, Zhu K, Shi D, Wang F, Cui G. Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers. PLoS One 2024; 19:e0309283. [PMID: 39231174 PMCID: PMC11373820 DOI: 10.1371/journal.pone.0309283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 08/09/2024] [Indexed: 09/06/2024] Open
Abstract
Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources.
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Affiliation(s)
- Hong Pan
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- Fangcheng Golden Camellia National Nature Reserve Management Center, Fangchenggang, China
| | - Libao Deng
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kaixian Zhu
- Scientific Research Academy of Guangxi Environmental Protection, Nanning, China
| | - Deju Shi
- Guangxi University, Nanning, China
| | - Feiyong Wang
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guofa Cui
- College of Nature Conservation, Beijing Forestry University, Beijing, China
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Angelakopoulos R, Tsipourlianos A, Giannoulis T, Mamuris Z, Moutou KA. MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass. Animals (Basel) 2024; 14:205. [PMID: 38254374 PMCID: PMC10812826 DOI: 10.3390/ani14020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.
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Affiliation(s)
- Rafael Angelakopoulos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Science, University of Thessaly, Greece Gaiopolis, 41334 Larissa, Greece;
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
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Surina B, Balant M, Glasnović P, Radosavljević I, Fišer Ž, Fujs N, Castro S. Population size as a major determinant of mating system and population genetic differentiation in a narrow endemic chasmophyte. BMC PLANT BIOLOGY 2023; 23:383. [PMID: 37553615 PMCID: PMC10411015 DOI: 10.1186/s12870-023-04384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND Mating system is one of the major determinants of intra- and interspecific genetic structure, but may vary within and between plant populations. Our study model included all known populations of Moehringia tommasinii (Caryophyllaceae), a narrow endemic plant inhabiting rock crevices in the northwestern Adriatic, and some populations of co-occurring and widespread M. muscosa, an ecologically divergent relative with an overlapping flowering period. We performed reciprocal crosses within and between taxa and used molecular markers to assess the extent of gene flow within and between populations and taxa. Using coefficient of inbreeding, population size, seed weight, pollen-to-ovule ratio, and flower display size, we also looked for evidence of a selfing syndrome. RESULTS A surprisingly high variation in mating systems was observed among populations of M. tommasinii. These populations exhibited genetic structuring, with their size positively correlated with both seed weight and pollen production. Although a selfing syndrome could not be confirmed as the majority of selfing resulted from allogamous treatments, the occurrence of selfing was notable. In the presence of M. muscosa, at a site where both species coexist closely, a distinct pattern of fruit production was observed in M. tommasinii following various pollination treatments. Molecular and morphometric data provided evidence of hybridization followed by local extinction at this site. CONCLUSIONS Population size proved to be the most important factor affecting the mating system in genetically structured populations of M. tommasinii. Lighter seeds and lower pollen production observed in populations with pronounced selfing do not provide enough evidence for the selfing syndrome. Detected gene flow between M. tommasinii and the sympatric M. muscosa suggested weak reproductive barriers between the taxa, which could pose a conservation problems for the former species. Hybridization leading to local extinction may also resulted in floral polymorphism and disruption of mating patterns of M. tommasinii.
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Affiliation(s)
- Boštjan Surina
- Natural History Museum Rijeka, Lorenzov prolaz 1, 51000, Rijeka, Croatia.
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Manica Balant
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038, Barcelona, Spain
| | - Peter Glasnović
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Ivan Radosavljević
- Division of Botany, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Živa Fišer
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Nataša Fujs
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Sílvia Castro
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
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Wang N, Cao S, Liu Z, Xiao H, Hu J, Xu X, Chen P, Ma Z, Ye J, Chai L, Guo W, Larkin RM, Xu Q, Morrell PL, Zhou Y, Deng X. Genomic conservation of crop wild relatives: A case study of citrus. PLoS Genet 2023; 19:e1010811. [PMID: 37339133 DOI: 10.1371/journal.pgen.1010811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.
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Affiliation(s)
- Nan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongjie Liu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Xiao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jianbing Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xiaodong Xu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Peng Chen
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhiyao Ma
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Wenwu Guo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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Ottati S, Eberle J, Rulik B, Köhler F, Ahrens D. From DNA barcodes to ecology: Meta-analysis of central European beetles reveal link with species ecology but also to data pattern and gaps. Ecol Evol 2022; 12:e9650. [PMID: 36568864 PMCID: PMC9771709 DOI: 10.1002/ece3.9650] [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: 09/12/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.
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Affiliation(s)
- Sara Ottati
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Jonas Eberle
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Environment & BiodiversityUniversity of SalzburgSalzburgAustria
| | - Björn Rulik
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Frank Köhler
- Coleopterological Research OfficeBornheimGermany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
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Srinivas Y, Yumnam B, Dutta S, Jhala Y. Assessing genetic diversity and population structure for prioritizing conservation of the critically endangered Great Indian Bustard (Aredotis nigriceps). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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8
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Feoktistova NY, Meschersky IG, Karmanova TN, Gureeva AV, Surov AV. Allele Diversity of the Major Histocompatibility Complex in the Common Hamster (Cricetus cricetus) in Urban and Rural Populations. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022050077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Bartolomé C, Buendía-Abad M, Ornosa C, De la Rúa P, Martín-Hernández R, Higes M, Maside X. Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae. MICROBIAL ECOLOGY 2022; 84:856-867. [PMID: 34609533 PMCID: PMC9622509 DOI: 10.1007/s00248-021-01882-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.
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Affiliation(s)
- Carolina Bartolomé
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.
| | - María Buendía-Abad
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Concepción Ornosa
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pilar De la Rúa
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, 30100, Murcia, Spain
| | - Raquel Martín-Hernández
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico Tecnológico de Albacete, 02006, Albacete, Spain
| | - Mariano Higes
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Xulio Maside
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain
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Applying novel connectivity networks to wood turtle populations to provide comprehensive conservation management strategies for species at risk. PLoS One 2022; 17:e0271797. [PMID: 35960725 PMCID: PMC9374220 DOI: 10.1371/journal.pone.0271797] [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: 08/25/2021] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Genetic diversity within and among populations is frequently used in prioritization processes to rank populations based on their vulnerability or distinctiveness, however, connectivity and gene flow are rarely considered within these frameworks. Using a wood turtle (Glyptemys insculpta) population graph, we introduce BRIDES as a new tool to evaluate populations for conservation purpose without focusing solely on individual nodes. BRIDES characterizes different types of shortest paths among the nodes of a subgraph and compares the shortest paths among the same nodes in a complete network. The main objectives of this study were to (1) introduce a BRIDES selection process to assist conservation biologists in the prioritization of populations, and (2) use different centrality indices and node removal statistics to compare BRIDES results and assess gene flow among wood turtle populations. We constructed six population subgraphs and used a stepwise selection algorithm to choose the optimal number of additional nodes, representing different populations, required to maximize network connectivity under different weighting schemes. Our results demonstrate the robustness of the BRIDES selection process for a given scenario, while inconsistencies were observed among node-based metrics. Results showed repeated selection of certain wood turtle populations, which could have not been predicted following only genetic diversity and distinctiveness estimation, node-based metrics and node removal analysis. Contrary to centrality measures focusing on static networks, BRIDES allowed for the analysis of evolving networks. To our knowledge, this study is the first to apply graph theory for turtle conservation genetics. We show that population graphs can reveal complex gene flow dynamics and population resiliency to local extinction. As such, BRIDES offers an interesting complement to node-based metrics and node removal to better understand the global processes at play when addressing population prioritization frameworks.
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Gene Flow and Recruitment Patterns among Disjunct Populations of Allocasuarina verticillata (Lam.) L.A.S. Johnson. FORESTS 2022. [DOI: 10.3390/f13071152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Allocasuarina verticillata (Lam.) L.A.S. Johnson is a widespread species in south-eastern Australia providing vegetation cover, protecting fragile soils and providing food for birds. Understanding the effects of gene flow on the recruitment patterns, genetic differentiation and structure of fragmented populations provides fundamental guidelines to underpin plant conservation strategies and activities. In this study, four spatially disjunct populations of A. verticillata were sampled to explore the effects of population size, reproductive patterns and pollen and seed dispersal on among-population genetic diversity, genetic differentiation and structure, using field survey and microsatellite marker techniques. It was found that stands of A. verticillata were predominantly sexually reproductive, but asexual reproduction through root suckering was an additional mode of reproduction. The reproductive success of A. verticillata is positively correlated with the effective population size rather than actual population size. The reduction in effective population size and increment of spatial isolation resulted in lower genetic diversity and higher inbreeding coefficient of progenies. Moderate pairwise genetic differentiation and weak genetic structure were identified. The results suggest that exogenous, wind-mediated pollen flow provides some maintenance of genetic diversity in the isolated stands. Seed dispersal appears mainly to be over short distances (i.e., within populations), but the infrequent transport of seeds between disjunct locations cannot be ruled out as another factor that may help maintain genetic diversity.
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Nguyen TN, Chen N, Cosgrove EJ, Bowman R, Fitzpatrick JW, Clark AG. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays, Aphelocoma coerulescens. Evol Appl 2022; 15:1018-1027. [PMID: 35782006 PMCID: PMC9234620 DOI: 10.1111/eva.13421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/04/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8-year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.
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Affiliation(s)
- Tram N. Nguyen
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
- Cornell Lab of OrnithologyIthacaNew YorkUSA
| | - Nancy Chen
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - Elissa J. Cosgrove
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Reed Bowman
- Avian Ecology LabArchbold Biological StationFloridaUSA
| | - John W. Fitzpatrick
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
- Cornell Lab of OrnithologyIthacaNew YorkUSA
| | - Andrew G. Clark
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
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13
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Buzan E, Potušek S, Duniš L, Pokorny B. Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals (Basel) 2022; 12:ani12060723. [PMID: 35327121 PMCID: PMC8944837 DOI: 10.3390/ani12060723] [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: 11/22/2021] [Revised: 02/23/2022] [Accepted: 03/10/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Disease prevention and appropriate wildlife management are among the major challenges in wildlife conservation. In the present study, we made a first assessment of the variability of major histocompatibility complex (MHC) genes in roe deer in Slovenia and evaluated local population adaptation by comparing MHC variability with neutral microsatellites. We discovered three new MHC DRB exon 2 alleles in addition to seven previously described in the literature. Moreover, we found evidence of historical positive selection, as selection analysis indicated that approx. 10% of the encoded amino acids were subjected to episodic positive selection. This study provides the basis for further research on immunogenetic variation in roe deer and highlights opportunities to incorporate genetic data into science-based population management. Abstract Disease control and containment in free-ranging populations is one of the greatest challenges in wildlife management. Despite the importance of major histocompatibility complex (MHC) genes for immune response, an assessment of the diversity and occurrence of these genes is still rare in European roe deer, the most abundant and widespread large mammal in Europe. Therefore, we examined immunogenetic variation in roe deer in Slovenia to identify species adaptation by comparing the genetic diversity of the MHC genes with the data on neutral microsatellites. We found ten MHC DRB alleles, three of which are novel. Evidence for historical positive selection on the MHC was found using the maximum likelihood codon method. Patterns of MHC allelic distribution were not congruent with neutral population genetic findings. The lack of population genetic differentiation in MHC genes compared to existing structure in neutral markers suggests that MHC polymorphism was influenced primarily by balancing selection and, to a lesser extent, by neutral processes such as genetic drift, with no clear evidence of local adaptation. Selection analyses indicated that approx. 10% of amino acids encoded under episodic positive selection. This study represents one of the first steps towards establishing an immunogenetic map of roe deer populations across Europe, aiming to better support science-based management of this important game species.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Correspondence: ; Tel.: +38-65-6117570; Fax: +38-65-61175
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Luka Duniš
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Boštjan Pokorny
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
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14
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Erofeeva MN, Alekseeva GS, Kim MD, Sorokin PA, Naidenko SV. Inbreeding Coefficient and Distance in MHC Genes of Parents as Predictors of Reproductive Success in Domestic Cat. Animals (Basel) 2022; 12:ani12020165. [PMID: 35049788 PMCID: PMC8772569 DOI: 10.3390/ani12020165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Inbreeding and low diversity in MHC (major histocompatibility complex) genes can have a significant impact on the survival and quality of offspring in mammals. At the same time, a decrease in genetic diversity can be disastrous for animals at individual and species level. For felines, studies of the effects of inbreeding and low variety in MHC genes are conducted on populations with a low number of animals, where there is a high probability of a shortage of available partners, and, accordingly, their choice. The use of model species, especially domestic cats, allows us to identify the main consequences of inbreeding and the lack of a choice of partners for future offspring. The survival of offspring in a domestic cat is primarily affected by the degree of similarity/difference in the genes of the parents’ MHC. Parents with the maximum distance in MHC genes have a larger proportion of surviving kittens, and this effect is most pronounced immediately after birth. In parents with the minimum distance in MHC genes, a significant percentage of kittens are either stillborn or die on the first day after birth. However, inbreeding and the similarity of parents in MHC genes in domestic cats did not affect the body mass of kittens. Abstract Inbreeding and low diversity in MHC genes are considered to have a negative effect on reproductive success in animals. This study presents an analysis of the number and body mass of offspring in domestic cat, depending on the inbreeding coefficient and the degree of similarity in MHC genes of class I and II in parents. Inbred partners had a lower number of live kittens at birth than outbred ones. At the same time, the inbreeding coefficient did not affect the litter size and the number of offspring who survived until the period of transition to solid food. The most significant predictor for the number of surviving offspring was the degree of parental similarity in MHC genes: the parents with the maximum distance in MHC genes had more survived kittens. Moreover, this effect was most pronounced immediately after birth. A significant percentage of kittens from parents with a minimum distance in MHC genes were either stillborn or died on the first day after birth. By the age of transition to solid food, this effect is no longer so pronounced. Furthermore, neither the inbreeding coefficient nor the distance in MHC genes of parents had any effect on the body mass of kittens.
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Affiliation(s)
- Mariya N. Erofeeva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; (G.S.A.); (P.A.S.); (S.V.N.)
- Correspondence:
| | - Galina S. Alekseeva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; (G.S.A.); (P.A.S.); (S.V.N.)
| | - Mariya D. Kim
- Department of Zoology, Institute of Zootechnics and Biology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str. 49, 127550 Moscow, Russia;
| | - Pavel A. Sorokin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; (G.S.A.); (P.A.S.); (S.V.N.)
| | - Sergey V. Naidenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; (G.S.A.); (P.A.S.); (S.V.N.)
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15
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Toczydlowski RH, Waller DM. Plastic and quantitative genetic divergence mirror environmental gradients among wild, fragmented populations of Impatiens capensis. AMERICAN JOURNAL OF BOTANY 2022; 109:99-114. [PMID: 34643270 DOI: 10.1002/ajb2.1782] [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: 02/22/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Habitat fragmentation generates molecular genetic divergence among isolated populations, but few studies have assessed phenotypic divergence and fitness in populations where the genetic consequences of habitat fragmentation are known. Phenotypic divergence could reflect plasticity, local adaptation, and/or genetic drift. METHODS We examined patterns and potential drivers of phenotypic divergence among 12 populations of jewelweed (Impatiens capensis) that show strong molecular genetic signals of isolation and drift among fragmented habitats. We measured morphological and reproductive traits in both maternal plants within natural populations and their self-fertilized progeny grown together in a common garden. We also quantified environmental divergence between home sites and the common garden. RESULTS Populations with less molecular genetic variation expressed less maternal phenotypic variation. Progeny in the common garden converged in phenotypes relative to their wild mothers but retained among-population differences in morphology, survival, and reproduction. Among-population phenotypic variance was 3-10× greater in home sites than in the common garden for 6 of 7 morphological traits measured. Patterns of phenotypic divergence paralleled environmental gradients in ways suggestive of adaptation. Progeny resembled their mothers less as the environmental distance between their home site and the common garden increased. CONCLUSIONS Despite strong molecular signatures of isolation and drift, phenotypic differences among these Impatiens populations appear to reflect both adaptive quantitative genetic divergence and plasticity. Quantifying the extent of local adaptation and plasticity and how these covary with molecular and phenotypic variation help us predict when populations may lose their adaptive capacity.
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Affiliation(s)
- Rachel H Toczydlowski
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Donald M Waller
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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16
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Åkesson M, Flagstad Ø, Aspi J, Kojola I, Liberg O, Wabakken P, Sand H. Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractTransboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.
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17
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Santiago-Ramos J, Feria-Toribio JM. Assessing the effectiveness of protected areas against habitat fragmentation and loss: A long-term multi-scalar analysis in a mediterranean region. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Reyne M, Dicks K, McFarlane C, Aubry A, Emmerson M, Marnell F, Reid N, Helyar S. Population genetic structure of the Natterjack toad (Epidalea calamita) in Ireland: implications for conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01421-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractMolecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.
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19
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Idnan M, Javid A, Tayyab M, Hussain A, Mansoor S, Bukhari SM, Irfan, Shahbaz M, Rehman KU, Andleeb S, Azam SM, Ali W. Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan. BRAZ J BIOL 2021; 83:e246322. [PMID: 34431908 DOI: 10.1590/1519-6984.246322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/02/2021] [Indexed: 11/22/2022] Open
Abstract
A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.
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Affiliation(s)
- M Idnan
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - M Tayyab
- University of Veterinary and Animal Sciences, Institute of Biochemistry and Biotechnology, Lahore, Pakistan
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Mansoor
- University of Central Punjab, Faculty of Life Sciences, Department of Microbiology, Lahore, Pakistan
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - Irfan
- Cholistan University of Veterinary and Animal Sciences, Department of Zoology, Lahore, Pakistan
| | - M Shahbaz
- Women University Azad Jamu and Kashmir, Department of Zoology, Bagh, Pakistan
| | - K Ur Rehman
- Govt. College Women University, Department of environmental Sciences, Sailkot, Pakistan
| | - S Andleeb
- Govt. College Women University, Department of environmental Sciences, Sailkot, Pakistan
| | - S M Azam
- University of Education, Department of Zoology, Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
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20
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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21
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Bell KC, Van Gunst J, Teglas MB, Hsueh J, Matocq MD. Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of Tamias amoenus. J Mammal 2021; 102:173-187. [DOI: 10.1093/jmammal/gyaa166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (Tamias amoenus celeris), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled T. amoenus and least chipmunks (T. minimus) from the isolated PFR and compared genetic diversity between these populations and more “mainland” populations, including other subspecies of chipmunks. Given the high frequency of hybridization in Tamias, we tested for hybridization between T. amoenus and T. minimus in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, Borrelia hermsii, to gain insight into population health. We found T. amoenus of the PFR are closely related to T. amoenus in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR T. amoenus are highly genetically differentiated from other populations. In contrast, PFR T. minimus had higher genetic diversity that was comparable to the other T. minimus population we sampled. Pathogen screening revealed that T. amoenus carried higher pathogen loads than T. minimus in the PFR, although the prevalence of infection was similar to other Tamias populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.
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Affiliation(s)
- Kayce C Bell
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, USA
| | | | - Mike B Teglas
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Mail Stop 202, Reno, NV USA
| | - Jennifer Hsueh
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Mail Stop 202, Reno, NV USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada, Mail Stop 186, Reno, NV, USA
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22
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Cambrone C, Cézilly F, Wattier R, Eraud C, Bezault E. Levels of genetic differentiation and gene flow between four populations of the Scaly-naped Pigeon, Patagioenas squamosa: implications for conservation. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2021. [DOI: 10.1080/01650521.2021.1878765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Christopher Cambrone
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
| | - Frank Cézilly
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
- Université d’Etat d’Haïti, Port-au-Prince, Haiti
| | - Rémi Wattier
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Cyril Eraud
- Office Français de la Biodiversité, Unité Avifaune Migratrice, Chizé, France
| | - Etienne Bezault
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
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23
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Do We Need to Identify Adaptive Genetic Variation When Prioritizing Populations for Conservation? CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01327-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Reyne M, Helyar S, Aubry A, Emmerson M, Marnell F, Reid N. Combining spawn egg counts, individual photo-ID and genetic fingerprinting to estimate the population size and sex ratio of an endangered amphibian. Integr Zool 2020; 16:240-254. [PMID: 33137231 DOI: 10.1111/1749-4877.12497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
According to the International Union for Conservation of Nature Red List, 41% of the world's amphibian species are threatened with extinction, making them more threatened than any other vertebrate group nowadays. Given the global amphibian crisis, comprehensive understanding of demographics and population trends of declining and threatened species is essential for effective management and conservation strategies. Counting egg spawns is widely used to assess population abundance in pond breeding anurans. However, it is unknown how such counts translate into robust population size estimations. We monitored the breeding activity of the Natterjack toad (Epidalea calamita), combining egg string counts and individual photo-identification with Capture-Mark-Recapture population size and operational sex ratio estimation. Male Natterjack toads were identified by the pattern of natural markings with repeated ID of the same individual confirmed for 10% of the samples using genetic fingerprinting. We identified 647 unique individuals within a closed study population at Caherdaniel, Co Kerry. Population estimates derived from egg string counts estimated a breeding population of 368 females (95% CI 353-384) and Capture-Mark-Recapture estimated a breeding population of 1698 males (95% CI 1000-2397). The female:male sex ratio was conservatively estimated at 1:5 (95% CI 1:3-1:6) where 62% ± 6% of females were assumed to spawn. These substantially departed from any priori assumption of 1:1 which could have underestimated the breeding population by up to 72%. Where amphibian absolute population size estimation is necessary, methods should include empirical survey data on operational sex ratios and not rely on assumptions or those derived from the literature which may be highly population and/or context-dependent.
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Affiliation(s)
- Marina Reyne
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Sarah Helyar
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Aurélie Aubry
- Agri-Food & Biosciences Institute (AFBI), Hillsborough, UK
| | - Mark Emmerson
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Ferdia Marnell
- National Parks & Wildlife Service (NPWS), Dublin, Ireland
| | - Neil Reid
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
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25
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Capblancq T, Butnor JR, Deyoung S, Thibault E, Munson H, Nelson DM, Fitzpatrick MC, Keller SR. Whole-exome sequencing reveals a long-term decline in effective population size of red spruce ( Picea rubens). Evol Appl 2020; 13:2190-2205. [PMID: 33005218 PMCID: PMC7513712 DOI: 10.1111/eva.12985] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/26/2020] [Accepted: 04/09/2020] [Indexed: 01/02/2023] Open
Abstract
Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo-genetic history can have immediate conservation implications. We used a whole-exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high-elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop "sky islands." Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome-derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small Ne , with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce.
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Affiliation(s)
| | - John R Butnor
- USDA Forest Service Southern Research Station University of Vermont Burlington VT USA
| | - Sonia Deyoung
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Ethan Thibault
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Helena Munson
- Department of Plant Biology University of Vermont Burlington VT USA
| | - David M Nelson
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Matthew C Fitzpatrick
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington VT USA
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Silva PIT, Silva-Junior OB, Resende LV, Sousa VA, Aguiar AV, Grattapaglia D. A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze. PLoS One 2020; 15:e0230404. [PMID: 32866150 PMCID: PMC7458329 DOI: 10.1371/journal.pone.0230404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.
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Affiliation(s)
- Pedro Italo T. Silva
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
| | - Orzenil B. Silva-Junior
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Lucileide V. Resende
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Valderes A. Sousa
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Ananda V. Aguiar
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
- Graduate Program in Genomic Sciences, Universidade Católica de Brasília, Brasília, DF, Brazil
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Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer S, Long JM, Eggert LS. Complex patterns of genetic and morphological differentiation in the Smallmouth Bass subspecies (Micropterus dolomieu dolomieu and M. d. velox) of the Central Interior Highlands. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01295-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nardelli M, Ibañez E, Dobler D, Illia G, Abba AM, Túnez JI. Genetic approach reveals a polygynous-polyandrous mating system and no social organization in a small and isolated population of the screaming hairy armadillo, Chaetophractus vellerosus. Genetica 2020; 148:125-133. [PMID: 32193750 DOI: 10.1007/s10709-020-00092-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 03/05/2020] [Indexed: 10/24/2022]
Abstract
The development of agro-ecosystems in the pastures of the Pampean Region has substantially modified their structure and functioning. Many wild mammal populations in the Argentinean Pampas face habitat loss and/or fragmentation due to human activities, resulting in harmful genetic effects. The screaming hairy armadillo (Chaetophractus vellerosus) is a species considered an indicator of the state of preservation of the environments it inhabits. However, very little information is available about its mating system in the wild. In this sense, an isolated population of the screaming hairy armadillo in the northeast of Buenos Aires Province, which is separated from the main distribution area of the species by about 500 km, requires special attention. Genetic studies that analyzed social behavior and mating systems in Xenarthra are scarce but necessary to establish conservation actions for the isolated screaming hairy armadillo population under study. Thus, we analyzed the existence of a possible social organization in the species, together with its mating system, using a set of previously characterized microsatellites. Our results showed a complex scenario for the dispersal and mating system in this C. vellerosus population. Males disperse and females have a philopatric tendency with some degree of dispersal. This strategy, in combination with a polygynous-polyandrous mating system, could enhance genetic variability in this small and isolated population. In addition, no evidence of social organization was found.
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Affiliation(s)
- Maximiliano Nardelli
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Argentina.
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Universidad Nacional de Luján, Luján, Argentina.
- Departamento de Educación, Universidad Nacional de Luján, Luján, Argentina.
| | - Ezequiel Ibañez
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Argentina
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Universidad Nacional de Luján, Luján, Argentina
| | - Dara Dobler
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Argentina
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Universidad Nacional de Luján, Luján, Argentina
| | - Gimena Illia
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Argentina
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Universidad Nacional de Luján, Luján, Argentina
| | - Agustín M Abba
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE), CCT-CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan Ignacio Túnez
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Argentina
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Universidad Nacional de Luján, Luján, Argentina
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Population structure and genetic diversity ofMagnolia cubensissubsp.acunae(Magnoliaceae): effects of habitat fragmentation and implications for conservation. ORYX 2020. [DOI: 10.1017/s003060531900053x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractGenetic data on threatened plant populations can facilitate the development of adequate conservation strategies to reduce extinction risk. Such data are particularly important for species affected by habitat fragmentation such asMagnolia cubensissubsp.acunae, a Critically Endangered magnolia subspecies endemic to Cuba. Using genetic data from 67 individuals, we aimed to evaluate the effect of habitat fragmentation on two subpopulations in the Guamuhaya mountain range, in Topes de Collantes Protected Natural Landscape and Lomas de Banao Ecological Reserve. We characterize the structure and genetic diversity of these subpopulations, with the objective of managing their conservation more effectively. We used Landsat satellite images to determine land-cover types at the two locations and calculated indices of habitat fragmentation. For genetic analyses, we extracted DNA from the leaf tissue of individuals from the two subpopulations and used 11 microsatellite markers to genotype them. We calculated heterozygosity, allelic richness and theF-statistics, to evaluate genetic variability. The montane rainforest in Topes de Collantes was most affected by habitat fragmentation, with smaller patches of more irregular shapes, compared to submontane forest at this location and both montane and submontane forests in Lomas de Banao. Genetic diversity was higher in Topes de Collantes, but we found no genetic differentiation between subpopulations. Our findings suggest the two subpopulations can be considered a single evolutionary unit and conservation entity. We propose to use individuals from both subpopulations for reinforcement to increase the overall genetic diversity of the subspecies.
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The Genetic Differentiation of Common Toads on UK Farmland: The Effect of Straight-Line (Euclidean) Distance and Isolation by Barriers in a Heterogeneous Environment. J HERPETOL 2020. [DOI: 10.1670/19-039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bortoluzzi C, Bosse M, Derks MFL, Crooijmans RPMA, Groenen MAM, Megens H. The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations. Evol Appl 2020; 13:330-341. [PMID: 31993080 PMCID: PMC6976952 DOI: 10.1111/eva.12872] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation and intense selective breeding. Here, we use whole-genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks for deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations.
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Affiliation(s)
- Chiara Bortoluzzi
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Mirte Bosse
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Martijn F. L. Derks
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Richard P. M. A. Crooijmans
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Martien A. M. Groenen
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
| | - Hendrik‐Jan Megens
- Department of Animal Sciences, Animal Breeding and GenomicsWageningen University & ResearchGelderlandThe Netherlands
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Tibihika PD, Curto M, Alemayehu E, Waidbacher H, Masembe C, Akoll P, Meimberg H. Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations. BMC Evol Biol 2020; 20:16. [PMID: 32000675 PMCID: PMC6990601 DOI: 10.1186/s12862-020-1583-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.
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Affiliation(s)
- Papius Dias Tibihika
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
| | - Esayas Alemayehu
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33/DG, 1180 Wien, Austria
| | - Herwig Waidbacher
- National Fishery and Aquatic Life Research Centre, P.O. Box 64, Addis Ababa, Sebeta Ethiopia
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Peter Akoll
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
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Tajchman K, Sawicka-Zugaj W, Greguła-Kania M, Drozd L, Czyżowski P. Effect of Translocations on the Genetic Structure in Populations of the Red Deer (Cervus elaphus) in Poland. RUSS J GENET+ 2020. [DOI: 10.1134/s102279541912010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Geographic Distribution of Chronic Wasting Disease Resistant Alleles in Nebraska, with Comments on the Evolution of Resistance. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2019. [DOI: 10.3996/012019-jfwm-002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Infectious diseases create major challenges for wildlife management. In particular, prion diseases are fatal and incurable, leaving managers with limited options. In cervids, chronic wasting disease (CWD) can decimate captive and wild populations by affecting neural tissue leading to body control loss, decay, and ultimately death resulting in ecological and economic consequences. Partial protection against CWD results from some genotypes at the prion (PRNP) locus encoding PrP proteins that are less likely to misfold and build up to fatal levels in the central nervous system. Although multiple studies have documented the association between CWD susceptibility and genotypes, little is known about the distribution of resistant genotypes across the natural landscape, and whether population pockets of protection in exist in particular regions. We surveyed the genetic variability and distribution of resistant alleles and genotypes of the PRNP locus across Nebraska in deer collected in 2017, where mule deer (Odocoileus hemionus) and white-tailed (O. virginianus) deer ranges meet on the North American Great Plains. We found that CWD-resistant alleles occur throughout the state in low frequencies, and our data suggest little evidence of geographic structure for the PRNP locus. In Nebraska, there is a lower frequency of the most common resistance allele (S96) compared with white-tailed deer in other parts of the Midwest. The frequency of resistant alleles (F225) was lower in mule deer. The low but widespread frequency of resistance alleles suggests that each species could be susceptible to CWD spread. Continued monitoring would be useful to determine if the frequency of resistant alleles increases in areas with increasing CWD rates. Three synonymous fixed genotypes at the PRNP locus allowed detection of hybrids between mule deer and white-tailed deer, although we found none, suggesting that CWD is not spread between species via hybridization. We also compare the PRNP genotypes of scrapie-resistant sheep with those of deer, and suggest that a single base-pair mutation at the PRNP locus could provide resistance in deer.
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Kalb DM, Delaney DA, DeYoung RW, Bowman JL. Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula. Ecol Evol 2019; 9:11504-11517. [PMID: 31641489 PMCID: PMC6802040 DOI: 10.1002/ece3.5655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 01/13/2023] Open
Abstract
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
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Affiliation(s)
- David M. Kalb
- Virginia Department of Game and Inland FisheriesMarionVAUSA
| | - Deborah A. Delaney
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTXUSA
| | - Jacob L. Bowman
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
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Population genetic structure of Bemisia tabaci MED (Hemiptera: Aleyrodidae) in Korea. PLoS One 2019; 14:e0220327. [PMID: 31344119 PMCID: PMC6657892 DOI: 10.1371/journal.pone.0220327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/12/2019] [Indexed: 11/19/2022] Open
Abstract
The sweet potato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a major agricultural pest that causes economic damages worldwide. In particular, B. tabaci MED (Mediterranean) has resulted in serious economic losses in tomato production of Korea. In this study, 1,145 B. tabaci MED females from 35 tomato greenhouses in different geographic regions were collected from 2016 to 2018 (17 populations in 2016, 13 in 2017, and five in 2018) and analyzed to investigate their population genetic structures using eight microsatellite markers. The average number of alleles per population (NA) ranged from 2.000 to 5.875, the expected heterozygosity (HE) ranged from 0.218 to 0.600, the observed heterozygosity (HO) ranged from 0.061 to 0.580, and the fixation index inbreeding coefficient (FIS) ranged from -0.391 to 0.872 over the three years of the study. Some significant correlation (p < 0.05) was present between genetic differentiations (FST) and geographical distance, and a comparatively high proportion of variation was found among the B. tabaci MED populations. The B. tabaci MED populations were divided into two well-differentiated genetic clusters within different geographic regions. Interestingly, its genetic structures converged into one genetic cluster during just one year. The reasons for this genetic change were speculated to arise from different fitness, insecticide resistance, and insect movement by human activities.
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Walls SC, Gabor CR. Integrating Behavior and Physiology Into Strategies for Amphibian Conservation. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00234] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Liu Y, Harris AJ, Gao Q, Su X, Ren Z. A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae). Ecol Evol 2019; 9:6014-6037. [PMID: 31161016 PMCID: PMC6540705 DOI: 10.1002/ece3.5186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/08/2022] Open
Abstract
We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among-species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.
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Affiliation(s)
- Yuping Liu
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - AJ Harris
- Department of BiologyOberlin College and ConservatoryOberlinOhio
| | - Qingbo Gao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
| | - Xu Su
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - Zhumei Ren
- School of Life ScienceShanxi UniversityTaiyuanChina
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39
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Ando H. Genetic and ecological conservation issues for oceanic island birds, revealed by a combination of the latest molecular techniques and conventional field work. Ecol Res 2019. [DOI: 10.1111/1440-1703.1062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies Ibaraki Japan
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40
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Adaptive marine conservation planning in the face of climate change: What can we learn from physiological, ecological and genetic studies? Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00566] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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41
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Tibihika PD, Curto M, Dornstauder-Schrammel E, Winter S, Alemayehu E, Waidbacher H, Meimberg H. Application of microsatellite genotyping by sequencing (SSR-GBS) to measure genetic diversity of the East African Oreochromis niloticus. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1136-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Sunde J, Tibblin P, Larsson P, Forsman A. Sex-specific effects of outbreeding on offspring quality in pike ( Esox lucius). Ecol Evol 2018; 8:10448-10459. [PMID: 30464817 PMCID: PMC6238122 DOI: 10.1002/ece3.4510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Intraspecific genetic admixture occurs when previously separated populations within a species start interbreeding, and it can have either positive, negative, or neutral effects on reproductive performance. As there currently is no reliable predictor for the outcome of admixture, an increased knowledge about admixture effects in different species and populations is important to increase the understanding about what determines the response to admixture. We tested for effects of admixture on F1 offspring quality in three subpopulations of pike (Esox lucius). Gametes were collected in the field, and eggs from each female were experimentally fertilized with milt from a male from each population (one "pure" and two "admixed" treatments). Three offspring quality measures (hatching success, fry survival, and fry length) were determined and compared between (a) pure and admixed population combinations and (b) the sex-specific treatments within each admixed population combination (based on the origin of the male and female, respectively). The results suggested that although there were no overall effects of admixture on offspring quality, the consequences for a given population combination could be sex-specific and thus differ depending on which of the parents originated from one or the other population. All offspring quality traits were influenced by both maternal ID and paternal ID. Sex- and individual-specific effects can have implications for dispersal behavior and gene flow between natural populations, and are important to consider in conservation efforts.
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Affiliation(s)
- Johanna Sunde
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Petter Tibblin
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Per Larsson
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
| | - Anders Forsman
- Department of Biology and Environmental ScienceEcology and Evolution in Microbial Model Systems, EEMiSLinnaeus UniversityKalmarSweden
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43
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Lee S, Kim B, Kim Y. Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations. Ecol Evol 2018; 8:8791-8802. [PMID: 30271546 PMCID: PMC6157670 DOI: 10.1002/ece3.4362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022] Open
Abstract
Distribution of genetic variation over time and space is relevant to demographic histories and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used eight microsatellite markers to examine the level of genetic diversity, spatial structure, and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within-population genetic variation associated with historical bottlenecks. Although pairwise F ST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broadscale spatial pattern of genetic structure. Bayesian clustering (best K = 6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045) and historical migration rates (2 × e-5-4.6 × e-4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.
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Affiliation(s)
- Soo‐Rang Lee
- Multidisciplinary Genome InstituteHallym UniversityChuncheon‐siKorea
| | - Bo‐Yun Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheon‐siKorea
| | - Young‐Dong Kim
- Department of Life SciencesHallym UniversityChuncheon‐siKorea
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44
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von Kohn C, Conrad K, Kramer M, Pooler M. Genetic diversity of Magnolia ashei characterized by SSR markers. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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45
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Jacobs SJ, Kristofferson C, Uribe‐Convers S, Latvis M, Tank DC. Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult. Mol Ecol 2018; 27:2397-2413. [DOI: 10.1111/mec.14590] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Sarah J. Jacobs
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Casey Kristofferson
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Simon Uribe‐Convers
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Maribeth Latvis
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - David C. Tank
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
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46
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Pearson SK, Bull CM, Gardner MG. Selection outweighs drift at a fine scale: Lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops. Mol Ecol 2018; 27:2204-2214. [PMID: 29603473 DOI: 10.1111/mec.14571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 11/30/2022]
Abstract
The highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with that at neutral genetic loci. Differences in MHC and neutral genetic variation are useful for inferring the relative influence of selection, gene flow and drift on MHC variation. To date, such investigations have usually been undertaken at a broad spatial scale. Yet, evolutionary and ecological processes can occur at a fine spatial scale, particularly in small or fragmented populations. We investigated spatial patterns of MHC variation among three geographically close, naturally discrete, sampling sites of Egernia stokesii, an Australian lizard. The MHC of E. stokesii has recently been characterized, and there is evidence for historical selection on the MHC. We found E. stokesii MHC weakly differentiated among sites compared to microsatellites, suggesting selection, acting similarly at each site, has outweighed any effects of low gene flow or of genetic drift on E. stokesii MHC variation. Our findings demonstrate the strength of selection in shaping patterns of MHC variation or consistency at a fine spatial scale.
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Affiliation(s)
- Sarah K Pearson
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - C Michael Bull
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia.,Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
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47
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Casas-Marce M, Marmesat E, Soriano L, Martínez-Cruz B, Lucena-Perez M, Nocete F, Rodríguez-Hidalgo A, Canals A, Nadal J, Detry C, Bernáldez-Sánchez E, Fernández-Rodríguez C, Pérez-Ripoll M, Stiller M, Hofreiter M, Rodríguez A, Revilla E, Delibes M, Godoy JA. Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA. Mol Biol Evol 2018; 34:2893-2907. [PMID: 28962023 PMCID: PMC5850336 DOI: 10.1093/molbev/msx222] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.
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Affiliation(s)
- Mireia Casas-Marce
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Begoña Martínez-Cruz
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Maria Lucena-Perez
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Antonio Rodríguez-Hidalgo
- Department of Prehistory, Complutense University, Madrid, Spain.,IDEA (Instituto de Evolución en África), Madrid, Spain.,Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain
| | - Antoni Canals
- Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain.,IPHES, Institut Català de Paleoecologia Humana i Evolució Social (Catalan Institute of Human Paleoecology and Social Evolution), Tarragona, Spain.,Area de Prehistoria (Department of Prehistory), Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleobiología, Instituto Andaluz del Patrimonio Histórico, Consejería de Cultura de la Junta de Andalucía, Seville, Spain
| | | | - Manuel Pérez-Ripoll
- Prehistory and Archaeology Department, University of Valencia, Valencia, Spain
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, Potsdam, Germany
| | - Alejandro Rodríguez
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Eloy Revilla
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Miguel Delibes
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - José A Godoy
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
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48
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Pratt EAL, Beheregaray LB, Bilgmann K, Zanardo N, Diaz-Aguirre F, Möller LM. Hierarchical metapopulation structure in a highly mobile marine predator: the southern Australian coastal bottlenose dolphin (Tursiops cf. australis). CONSERV GENET 2018. [DOI: 10.1007/s10592-017-1043-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Mannise N, Cosse M, González S, Emmons LH, Barbanti Duarte JM, Beccaceci MD, Maldonado JE. Maned wolves retain moderate levels of genetic diversity and gene flow despite drastic habitat fragmentation. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00859] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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50
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Conservation genetics of eastern hellbenders Cryptobranchus alleganiensis alleganiensis in the Tennessee Valley. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1033-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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