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Liu L, James J, Zhang YQ, Wang ZF, Arakaki M, Vadillo G, Zhou QJ, Lascoux M, Ge XJ. The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity? THE NEW PHYTOLOGIST 2024; 244:277-291. [PMID: 39135394 DOI: 10.1111/nph.20036] [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: 02/13/2024] [Accepted: 07/16/2024] [Indexed: 09/17/2024]
Abstract
Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
| | - Jennifer James
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
- Swedish Collegium of Advanced Study, Uppsala University, Uppsala, 75236, Sweden
| | - Yu-Qu Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712044, China
| | - Zheng-Feng Wang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mónica Arakaki
- Natural History Museum, Universidad Nacional Mayor de San Marcos, Lima, 15072, Peru
| | - Giovana Vadillo
- Plant Physiology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, 15081, Peru
| | - Qiu-Jie Zhou
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
| | - Xue-Jun Ge
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
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2
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Kapsetaki SE, Compton ZT, Mellon W, Vincze O, Giraudeau M, Harrison TM, Abegglen LM, Boddy AM, Maley CC, Schiffman JD. Germline mutation rate predicts cancer mortality across 37 vertebrate species. Evol Med Public Health 2024; 12:122-128. [PMID: 39233763 PMCID: PMC11372239 DOI: 10.1093/emph/eoae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Background and objectives Cancer develops across nearly every species. However, cancer occurs at unexpected and widely different rates throughout the animal kingdom. The reason for this variation in cancer susceptibility remains an area of intense investigation. Cancer evolves in part through the accumulation of mutations, and therefore, we hypothesized that germline mutation rates would be associated with cancer prevalence and mortality across species. Methodology We collected previously published data on germline mutation rate and cancer mortality data for 37 vertebrate species. Results Germline mutation rate was positively correlated with cancer mortality (P-value = 0.0008; R2 = 0.13). Controlling for species' average parental age, maximum longevity, adult body mass or domestication did not improve the model fit (the change (Δ) in Akaike Information Criterion (AIC) was less than 2). However, this model fit was better than a model controlling for species trophic level (ΔAIC > 2). Conclusions and implications The increased death rate from cancer in animals with increased germline mutation rates may suggest underlying hereditary cancer predisposition syndromes similar to those diagnosed in human patients. Species with higher germline mutation rates may benefit from close monitoring for tumors due to increased genetic risk for cancer development. Early diagnoses of cancer in these species may increase their chances of overall survival, especially for threatened and endangered species.
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Affiliation(s)
- Stefania E Kapsetaki
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Center for Biocomputing, Security and Society, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Biology, School of Arts and Sciences, Tufts University, Medford, MA, USA
| | - Zachary T Compton
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- University of Arizona Cancer Center, Tucson, AZ, USA
- University of Arizona College of Medicine, Tucson, AZ, USA
| | - Walker Mellon
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
| | - Orsolya Vincze
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Institute of Aquatic Ecology, Centre for Ecological Research, Debrecen, Hungary
| | - Mathieu Giraudeau
- Littoral Environnement Et Sociétés (LIENSs), UMR7266, CNRS Université de La Rochelle, 2 rue Olympe de Gouges, 17042 La Rochelle Cedex, France
| | - Tara M Harrison
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC 27607, USA
- Exotic Species Cancer Research Alliance, North Carolina State University, Raleigh, NC 27607, USA
| | - Lisa M Abegglen
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Exotic Species Cancer Research Alliance, North Carolina State University, Raleigh, NC 27607, USA
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Peel Therapeutics, Inc., Salt Lake City, UT, USA
| | - Amy M Boddy
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Exotic Species Cancer Research Alliance, North Carolina State University, Raleigh, NC 27607, USA
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Center for Biocomputing, Security and Society, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Joshua D Schiffman
- Arizona Cancer Evolution Center, Arizona State University, Tempe, AZ, USA
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Peel Therapeutics, Inc., Salt Lake City, UT, USA
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3
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Lee S, Hwang S, Lee M, Seung J, Choi W, Bai M. DNA barcoding reveals a taxonomic fraud: Note on validity of Propomacrusmuramotoae (Coleoptera, Scarabaeidae). Zookeys 2024; 1206:181-190. [PMID: 39015529 PMCID: PMC11249845 DOI: 10.3897/zookeys.1206.124932] [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: 04/08/2024] [Accepted: 05/28/2024] [Indexed: 07/18/2024] Open
Abstract
Until the early 2000s, the genus Propomacrus was known to comprise two species, occurring in the Eastern Mediterranean and Southeast China. The discovery of Propomacrusmuramotoae Fujioka in Tibet and subsequently in Bhutan and Nepal, might play a crucial role in bridging the geographical distribution gap of the Euchirini tribe between the Mediterranean and Central China, offering profound insights into its evolution and biogeography. However, all specimens, including the holotype specimen, were sourced from a single insect vendor, with no further specimens found or catalogued in museum collections thereafter. During our examination of a P.muramotoae specimen from a private collection in South Korea, we found its COI gene sequence to be identical to that of P.bimucronatus (Pallas) from Turkey, a species known for its wide distribution and genetic variability across regional populations. This overlap in genetic identity raised significant doubts, further compounded by our detection of deliberate modifications in essential diagnostic features during morphological examination. All three specimens we examined showed crude modifications, including staining and artificial grinding. Despite our inability to access the P.muramotoae type specimens for direct examination-a challenge we attempted to overcome through various means-it is evident that significant fraudulent tampering has occurred with the P.muramotoae specimens. Therefore, a new synonymy is proposed: Propomacrusbimucronatus Pallas, 1781 = P.muramotoae Fujioka, 2007 (syn. nov.). We also advocate for a straightforward verification of the type specimen through molecular analysis of the COI barcode region and morphological re-examination under a microscope for those who have access to the type specimens.
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Affiliation(s)
- Seunghyun Lee
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Department of Life Sciences, Natural History Museum, London, UKNatural History MuseumLondonUnited Kingdom
| | - Seulmaro Hwang
- Department of Science Contents, Visang Education, Gwacheon, Republic of KoreaVisang EducationGwacheonRepublic of Korea
| | - Minhyeuk Lee
- National Institute of Agricultural Sciences, Wanju, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of KoreaNational Institute of Agricultural SciencesWanjuRepublic of Korea
| | - Jinbae Seung
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of KoreaNational Institute of Agricultural SciencesWanjuRepublic of Korea
| | - Woong Choi
- 305-403, Sechangnamsunhwan-ro, Namdong-gu, Incheon, Republic of KoreaUnaffiliatedIncheonRepublic of Korea
| | - Ming Bai
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing, ChinaUniversity of Chinese Academy of SciencesBeijingChina
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4
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Maxwell LM, Clark JD, Walsh J, Conway M, Olsen BJ, Kovach AI. Ecological characteristics explain neutral genetic variation of three coastal sparrow species. Mol Ecol 2024; 33:e17316. [PMID: 38481075 DOI: 10.1111/mec.17316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.
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Affiliation(s)
- Logan M Maxwell
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jonathan D Clark
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York, USA
| | - Meaghan Conway
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
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5
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Stubbs RL, Theodoridis S, Mora-Carrera E, Keller B, Potente G, Yousefi N, Jay P, Léveillé-Bourret É, Choudhury RR, Celep F, Kochjarová J, Conti E. The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries. THE NEW PHYTOLOGIST 2024; 241:911-925. [PMID: 37921572 DOI: 10.1111/nph.19361] [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: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries.
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Affiliation(s)
- Rebecca L Stubbs
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, 60325, Germany
| | - Emiliano Mora-Carrera
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Étienne Léveillé-Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montreal, QC, H1X 2B2, Canada
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, 71450, Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University in Zvolen, Zvolen, 96001, Slovak Republic
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
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6
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Samake JN, Lavretsky P, Gunarathna I, Follis M, Brown JI, Ali S, Yared S, Carter TE. Population genomic analyses reveal population structure and major hubs of invasive Anopheles stephensi in the Horn of Africa. Mol Ecol 2023; 32:5695-5708. [PMID: 37795951 DOI: 10.1111/mec.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/15/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome-wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation-by-distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype-environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.
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Affiliation(s)
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | | | - Madison Follis
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Joshua I Brown
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Said Ali
- Ministry of Health Somaliland, Hargeisa, Somalia
| | - Solomon Yared
- Department of Biology, Jigjiga University, Jigjiga, Ethiopia
| | - Tamar E Carter
- Department of Biology, Baylor University, Waco, Texas, USA
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7
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Fang X, Dong D, Yang M, Li X. Phylogenetics and Population Genetics of the Petrolisthes lamarckii-P. haswelli Complex in China: Old Lineage and New Species. Int J Mol Sci 2023; 24:15843. [PMID: 37958829 PMCID: PMC10648172 DOI: 10.3390/ijms242115843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii-P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents.
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Affiliation(s)
- Xuefeng Fang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Dong
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Yang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
| | - Xinzheng Li
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.F.); (M.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laoshan Laboratory, Qingdao 266237, China
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8
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Zhao P, Zhang L, Liu Y, Wang Z, Guo H, Li J, Wu S, Gao Z, Yuan H. Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers. Anim Biotechnol 2023; 35:2276717. [PMID: 37934003 DOI: 10.1080/10495398.2023.2276717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The objective of this study was to assess the genetic diversity, phylogenetic relationship and population structure of five goat breeds in Shanxi, China. High genetic diversities were found in the five populations, among which, Licheng big green goat (LCBG) has the highest genetic diversity, while Jinlan cashmere goat (JLCG) population has the lowest genetic diversity. Bottleneck analysis showed the absence of recent genetic bottlenecks in the five goat populations. Genetic differentiation analysis shows that the closest genetic relationship between LCBG and LLBG (Lvliang black goat) was found, and the genetic distance between JLCG and the other four populations is the largest. The population structure of JLCG is different from the other four populations with K = 2, while LCBG and LLBG have high similarity population structure as the K value changes. Knowledge about genetic diversity and population structure of indigenous goats is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds.
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Affiliation(s)
- Peng Zhao
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Li Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Yin Liu
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Zhengkun Wang
- Shanxi Animal Husbandry Technology Popularization Service Center, Taiyuan, China
| | - Hongyu Guo
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Jun Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Shuai Wu
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Zefeng Gao
- Agriculture and Rural Bureau of Lvliang City, Lvliang, Shanxi Province, China
| | - Hao Yuan
- Animal Husbandry Center of Yangcheng County, Jincheng, Shanxi Province, China
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9
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Winker K, Withrow JJ, Gibson DD, Pruett CL. Beringia as a high-latitude engine of avian speciation. Biol Rev Camb Philos Soc 2023; 98:1081-1099. [PMID: 36879465 DOI: 10.1111/brv.12945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Jack J Withrow
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Daniel D Gibson
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Christin L Pruett
- Department of Biology, Ouachita Baptist University, 410 Ouachita St, Arkadelphia, AR, 71998, USA
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Laojun S, Changbunjong T, Sumruayphol S, Chaiphongpachara T. Molecular and morphometric differentiation of secondary filariasis vector Coquillettidia mosquitoes (Diptera: Culicidae) in Thailand. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105452. [PMID: 37257802 DOI: 10.1016/j.meegid.2023.105452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Coquillettidia mosquitoes are important nuisance-biting pests and a vector of brugian filariasis in Thailand. However, comprehensive information about these mosquitoes remains unavailable such as molecular and morphometric differences among species. The lack of vector knowledge on Coquillettidia species could affect future disease control. This study aims to investigate differences in molecular variations based on mitochondrial cytochrome oxidase subunit I (COI) gene and wing geometric traits of three Coquillettidia species, namely Cq. crassipes, Cq. nigrosignata, and Cq. ochracea in Thailand. The results of molecular analyses revealed the differences among three Coquillettidia species. The genetic difference measure based on the Kimura two-parameter model among three Coquillettidia species showed low intraspecific distances (0%-3.05%) and large interspecific distances (10.10%-12.41%). The values of intra- and inter-genetic differences of three Coquillettidia species did not overlap which showed the existence of a barcoding gap indicating the efficiency of the identification based on the COI gene. As with molecular analysis, the landmark-based geometric morphometrics approach based on wing shape analysis indicated three distinct species groups which were supported by the high total performance score of cross-validated classification (97.16%). These results provide the first evidence of taxonomic signal based on molecular and wing geometric differences to support species identification and biological variations of Coquillettidia mosquitoes in Thailand for understanding these rare vector mosquitoes in depth and leading to effective further mosquito control.
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Affiliation(s)
- Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Ra-jabhat University, Samut Songkhram 75000, Thailand
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Suchada Sumruayphol
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Ra-jabhat University, Samut Songkhram 75000, Thailand.
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11
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Hoffman JR, Karol KG, Ohmura Y, Pogoda CS, Keepers KG, McMullin RT, Lendemer JC. Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales. Mycologia 2023; 115:187-205. [PMID: 36736327 DOI: 10.1080/00275514.2022.2157665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.
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Affiliation(s)
- Jordan R Hoffman
- Department of Biology, The City University of New York Graduate Center, 365 5th Avenue, New York, New York 10016
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Kenneth G Karol
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Yoshihito Ohmura
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Japan
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Richard T McMullin
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - James C Lendemer
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
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12
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Gajdárová B, Belotti E, Bufka L, Volfová J, Wölfl S, Mináriková T, Hollerbach L, Duľa M, Kleven O, Kutal M, Nowak C, Ozoliņš J, Tám B, Bryja J, Koubek P, Krojerová-Prokešová J. Long-term genetic monitoring of a reintroduced Eurasian lynx population does not indicate an ongoing loss of genetic diversity. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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13
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Rodrigues BL, Galati EAB. Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review. Acta Trop 2023; 238:106778. [PMID: 36435214 DOI: 10.1016/j.actatropica.2022.106778] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.
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Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904.
| | - Eunice Aparecida Bianchi Galati
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904
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14
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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15
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Mamat M, Shan W, Dong P, Zhou S, Liu P, Meng Y, Nie W, Teng P, Zhang Y. Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers. Front Genet 2022; 13:1018632. [PMID: 37006991 PMCID: PMC10064446 DOI: 10.3389/fgene.2022.1018632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.
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16
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Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales. Sci Rep 2022; 12:21064. [PMID: 36473926 PMCID: PMC9726941 DOI: 10.1038/s41598-022-25565-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).
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17
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Imwattana K, Aguero B, Duffy A, Shaw AJ. Demographic history and gene flow in the peatmosses Sphagnum recurvum and Sphagnum flexuosum (Bryophyta: Sphagnaceae). Ecol Evol 2022; 12:e9489. [PMID: 36407896 PMCID: PMC9667404 DOI: 10.1002/ece3.9489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/28/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
Population size changes and gene flow are processes that can have significant impacts on evolution. The aim of this study was to investigate the relationship of geography to patterns of gene flow and population size changes in a pair of closely related Sphagnum (peatmoss) species: S. recurvum and S. flexuosum. Both species occur in eastern North America, and S. flexuosum also occurs in Europe. Genetic data from restriction-site-associated DNA sequencing (RAD-seq) were used in this study. Analyses of gene flow were accomplished using coalescent simulations of site frequency spectra (SFSs). Signatures of gene flow were confirmed by f 4 statistics. For S. flexuosum, genetic diversity of plants in glaciated areas appeared to be lower than that in unglaciated areas, suggesting that glaciation can have an impact on effective population sizes. There is asymmetric gene flow from eastern North America to Europe, suggesting that Europe might have been colonized by plants from eastern North America after the last glacial maximum. The rate of gene flow between S. flexuosum and S. recurvum is lower than that between geographically disjunct S. flexuosum populations. The rate of gene flow between species is higher among sympatric plants of the two species than between currently allopatric S. flexuosum populations. There was also gene flow from S. recurvum to the ancestor S. flexuosum on both continents which occurred through secondary contact. These results illustrate a complex history of interspecific gene flow between S. flexuosum and S. recurvum, which occurred in at least two phases: between ancestral populations after secondary contact and between currently sympatric plants.
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Affiliation(s)
- Karn Imwattana
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - Aaron Duffy
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - A. Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
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18
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Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum. Appl Environ Microbiol 2022; 88:e0061722. [PMID: 35867580 PMCID: PMC9317897 DOI: 10.1128/aem.00617-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (Ne) has tracked changes in the population of its roe deer host. Specifically, both host and bacterium have undergone substantial increases in Ne over the past 1,500 years. In contrast, we show that while it appears to have undergone a major population expansion starting ~3,500 years ago, in the past 500 years, the contemporary host generalist ecotype has experienced a substantial reduction in genetic diversity levels, possibly as a result of reduced opportunities for transmission between competent hosts. IMPORTANCE The findings of this study reveal specific events important for the evolution of host specialization in a naturally occurring, obligately intracellular bacterial pathogen. Specifically, they show that host range shifts and the emergence of host specialization may occur during periods of population growth in a generalist ancestor. Our results also demonstrate the close correlation between demographic patterns in host and pathogen for a specialist system. These findings have important relevance for understanding the evolution of host range diversity. They may inform future work on host range dynamics, and they provide insights for understanding the emergence of pathogens that have human and veterinary health implications.
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19
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal AM, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Di Santo LN, Hoban S, Parchman TL, Wright JW, Hamilton JA. Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation. Mol Ecol 2022; 31:4622-4639. [PMID: 35822858 DOI: 10.1111/mec.16615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
Understanding the contribution of neutral and adaptive evolutionary processes to population differentiation is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to identify loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation within both Torrey pine populations, reflecting consistently low effective population sizes across time, and limited genetic differentiation, suggesting maintenance of gene flow between populations following divergence. However, genome scans identified more than 2000 candidate SNPs potentially under divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, evidence for adaptive differentiation suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.
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Affiliation(s)
- Lionel N Di Santo
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA
| | | | | | - Jessica W Wright
- USDA- Forest Service, Pacific Southwest Research Station, Davis, CA, USA
| | - Jill A Hamilton
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA.,Pennsylvania State University, Department of Ecosystem Science and Management, University Park, PA, USA
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21
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Ramirez JL, Lescroart J, Figueiró HV, Torres-Florez JP, Villela PMS, Coutinho LL, Freitas PD, Johnson WE, Antunes A, Galetti PM, Eizirik E. Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats. Mol Biol Evol 2022; 39:6594307. [PMID: 35639983 PMCID: PMC9189605 DOI: 10.1093/molbev/msac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, e.g. a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Peru
| | - Jonas Lescroart
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henrique V Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, USA
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade/Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (ICMBio/CMA), Santos, Brazil
| | | | - Luiz L Coutinho
- Centro de Genômica Funcional, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Patricia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil.,INCT-EECBio, Goiânia, GO, Brazil
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22
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Dellinger AS, Paun O, Baar J, Temsch EM, Fernández‐Fernández D, Schönenberger J. Population structure in Neotropical plants: Integrating pollination biology, topography and climatic niches. Mol Ecol 2022; 31:2264-2280. [PMID: 35175652 PMCID: PMC9310734 DOI: 10.1111/mec.16403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/29/2022]
Abstract
Animal pollinators mediate gene flow among plant populations, but in contrast to well-studied topographic and (Pleistocene) environmental isolating barriers, their impact on population genetic differentiation remains largely unexplored. Comparing how these multifarious factors drive microevolutionary histories is, however, crucial for better resolving macroevolutionary patterns of plant diversification. Here we combined genomic analyses with landscape genetics and niche modelling across six related Neotropical plant species (424 individuals across 33 localities) differing in pollination strategy to test the hypothesis that highly mobile (vertebrate) pollinators more effectively link isolated localities than less mobile (bee) pollinators. We found consistently higher genetic differentiation (FST ) among localities of bee- than vertebrate-pollinated species with increasing geographical distance, topographic barriers and historical climatic instability. High admixture among montane populations further suggested relative climatic stability of Neotropical montane forests during the Pleistocene. Overall, our results indicate that pollinators may differentially impact the potential for allopatric speciation, thereby critically influencing diversification histories at macroevolutionary scales.
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Affiliation(s)
- Agnes S. Dellinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
- Ecology and Evolutionary BiologyUniversity of ColoradoBoulderUSA
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | - Eva M. Temsch
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaWienAustria
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23
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Pilger TJ, Gido KB, Propst DL, Whitney JE, Turner TF. Demography predicts genetic effective size in a desert stream fish community. Am Nat 2022; 200:275-291. [DOI: 10.1086/720208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Devillard S, Jacquier M, Vandel JM, Léger F, Duhayer J, Pardonnet S, Say L, Ruette S. Genetic variability and population size covary positively across nine badgers (Meles meles) populations in France. MAMMAL RES 2022. [DOI: 10.1007/s13364-021-00614-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers. Animals (Basel) 2022; 12:ani12020148. [PMID: 35049770 PMCID: PMC8772547 DOI: 10.3390/ani12020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in 72 individuals of Varanus salvator macromaculatus and other varanids have been observed. Divergence of the two CRs from each individual revealed a pattern of independent evolution in CRs of varanid lineage. This study is a first step towards developing new phylogenetic evolutionary models of the varanid lineage, with accurate evolutionary inferences to provide basic insights into the biology of mitogenomes. Abstract Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.
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Hardianto E, Permata Wijayanti D, Shy JY, Mather P, Hughes J, Imai H. Molecular ecology of the fiddler crab Austruca perplexa (H. Milne Edwards, 1852): genetic divergence along a major biogeographical barrier, Wallace’s Line. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Genetic diversity and population structure in the fiddler crab Austruca perplexa were investigated to acquire a better understanding of the evolutionary history of the species. Nucleotide sequence analysis was performed from a polymerase chain reaction-amplified fragment of the mitochondrial DNA control region. A 691 bp nucleotide sequence was obtained from 618 specimens collected from 13 sites across Japan, Taiwan, the Philippines, Indonesia and Australia. Haplotype diversity ranged from 0.8 to 0.99, and nucleotide diversity values were lower (range, 0.30–1.9%) than those reported previously for other crustacean taxa. Gene flow was evident within populations in Japan and western Indonesia, but absent among all other populations, including eastern Indonesia. This pattern conforms to the one observed in many other marine taxa across the major biogeographical region referred to as Wallacea. The population pairwise fixation index (FST) and FST P-values were high and significant among many sites, implying that gene flow is restricted among most of the geographical regions sampled here. We hypothesize that physical oceanic barriers coupled with a short pelagic larval duration are responsible for creating the patterns we found. Strong evidence for population structure in a species that has relatively high dispersal potential, resulting in among-population differentiation, is a potential driver of evolutionary novelty. Our results provide a foundation for developing better conservation strategies for this widespread intertidal species.
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Affiliation(s)
- Eko Hardianto
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Central Java, Indonesia
| | - Diah Permata Wijayanti
- Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Central Java, Indonesia
| | - Jhy-Yun Shy
- Department of Aquaculture, College of Marine Resource and Engineering, National Penghu University of Science and Technology, Magong, Penghu, Taiwan
| | - Peter Mather
- Australian Rivers Institute, Griffith University, Nathan, Brisbane, QLD, Australia
| | - Jane Hughes
- Australian Rivers Institute, Griffith University, Nathan, Brisbane, QLD, Australia
| | - Hideyuki Imai
- Laboratory of Marine Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
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Benovics M, Gettová L, Šimková A. De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea): Revealing the phylogeographic pattern of population structure in the generalist parasite Dactylogyrus vistulae. Ecol Evol 2021; 11:16585-16599. [PMID: 34938459 PMCID: PMC8668815 DOI: 10.1002/ece3.8230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022] Open
Abstract
Approaches using microsatellite markers are considered the gold standard for modern population genetic studies. However, although they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species Dactylogyrus vistulae. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among D. vistulae individuals in the southern Balkans (mean N A per locus = 3.917), suggesting that generalist D. vistulae expanded from the south to the north in the Balkans and later into central Europe. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of D. vistulae is associated with the diversification of their cyprinoid hosts. In addition, the partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier for gene flow, even for generalist parasite species.
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Affiliation(s)
- Michal Benovics
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Lenka Gettová
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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Faillace CA, Sentis A, Montoya JM. Eco-evolutionary consequences of habitat warming and fragmentation in communities. Biol Rev Camb Philos Soc 2021; 96:1933-1950. [PMID: 33998139 PMCID: PMC7614044 DOI: 10.1111/brv.12732] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 01/17/2023]
Abstract
Eco-evolutionary dynamics can mediate species and community responses to habitat warming and fragmentation, two of the largest threats to biodiversity and ecosystems. The eco-evolutionary consequences of warming and fragmentation are typically studied independently, hindering our understanding of their simultaneous impacts. Here, we provide a new perspective rooted in trade-offs among traits for understanding their eco-evolutionary consequences. On the one hand, temperature influences traits related to metabolism, such as resource acquisition and activity levels. Such traits are also likely to have trade-offs with other energetically costly traits, like antipredator defences or dispersal. On the other hand, fragmentation can influence a variety of traits (e.g. dispersal) through its effects on the spatial environment experienced by individuals, as well as properties of populations, such as genetic structure. The combined effects of warming and fragmentation on communities should thus reflect their collective impact on traits of individuals and populations, as well as trade-offs at multiple trophic levels, leading to unexpected dynamics when effects are not additive and when evolutionary responses modulate them. Here, we provide a road map to navigate this complexity. First, we review single-species responses to warming and fragmentation. Second, we focus on consumer-resource interactions, considering how eco-evolutionary dynamics can arise in response to warming, fragmentation, and their interaction. Third, we illustrate our perspective with several example scenarios in which trait trade-offs could result in significant eco-evolutionary dynamics. Specifically, we consider the possible eco-evolutionary consequences of (i) evolution in thermal performance of a species involved in a consumer-resource interaction, (ii) ecological or evolutionary changes to encounter and attack rates of consumers, and (iii) changes to top consumer body size in tri-trophic food chains. In these scenarios, we present a number of novel, sometimes counter-intuitive, potential outcomes. Some of these expectations contrast with those solely based on ecological dynamics, for example, evolutionary responses in unexpected directions for resource species or unanticipated population declines in top consumers. Finally, we identify several unanswered questions about the conditions most likely to yield strong eco-evolutionary dynamics, how better to incorporate the role of trade-offs among traits, and the role of eco-evolutionary dynamics in governing responses to warming in fragmented communities.
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Affiliation(s)
- Cara A. Faillace
- Theoretical and Experimental Ecology Station, French National Centre of Scientific Research (CNRS), 2 Route du CNRS, Moulis, 09200, France,Address for correspondence (Tel: +33 5 61 04 05 89; )
| | - Arnaud Sentis
- Theoretical and Experimental Ecology Station, French National Centre of Scientific Research (CNRS), 2 Route du CNRS, Moulis, 09200, France,INRAE, Aix Marseille University, UMR RECOVER, 3275 Route de Cézanne- CS 40061, Aix-en-Provence Cedex 5, 13182, France
| | - José M. Montoya
- Theoretical and Experimental Ecology Station, French National Centre of Scientific Research (CNRS), 2 Route du CNRS, Moulis, 09200, France
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Donati GFA, Zemp N, Manel S, Poirier M, Claverie T, Ferraton F, Gaboriau T, Govinden R, Hagen O, Ibrahim S, Mouillot D, Leblond J, Julius P, Velez L, Zareer I, Ziyad A, Leprieur F, Albouy C, Pellissier L. Species ecology explains the spatial components of genetic diversity in tropical reef fishes. Proc Biol Sci 2021; 288:20211574. [PMID: 34583586 PMCID: PMC8479362 DOI: 10.1098/rspb.2021.1574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/03/2021] [Indexed: 11/12/2022] Open
Abstract
Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.
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Affiliation(s)
- Giulia Francesca Azzurra Donati
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zürich, CH8092 Zürich, Switzerland
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
| | - Maude Poirier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Thomas Claverie
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Centre Universitaire de formation et de recherche de Mayotte, Dembeni 97660, France
| | - Franck Ferraton
- Centre National de la Recherche Scientifique (CNRS), UMR 248 MARBEC, Montpellier, France
| | - Théo Gaboriau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | | | - Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Shameel Ibrahim
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - David Mouillot
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Julien Leblond
- Wildlife Conservation Society, Madagascar Program, Antananarivo, Madagascar
| | | | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
| | - Irthisham Zareer
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - Adam Ziyad
- Ministry of Fisheries and Agriculture, Malé, Republic of Maldives
| | - Fabien Leprieur
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Institut Universitaire de France, Paris, France
| | - Camille Albouy
- IFREMER, Unité Écologie et Modèles pour l'Halieutique, rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 3, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
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Clinging to survival: Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum persists in shrinking forest patches. ORYX 2021. [DOI: 10.1017/s0030605320000952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractThe Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining forest patches and assess deforestation. We then surveyed forest patches for the presence of this chameleon, and assessed its genetic diversity and structure. We estimated that 80% of the forest has been destroyed since 1984, although we found extant populations of the chameleon in each of the patches surveyed. Differentiation of genetic structure was strong between populations, suggesting that gene flow has been impaired. Genetic diversity was not low, but this could be the result of a temporal lag as well as lack of sensitivity in the mitochondrial marker used. Overall, the impact of forest loss is assumed to have led to a large demographic decline, with forest fragmentation preventing gene flow.
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High Genetic Diversity and Low Population Differentiation in Wild Hop (Humulus lupulus L.) from Croatia. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hop (Humulus lupulus L.) is used in the brewing industry as a source of compounds responsible for the bitterness, aroma, and preservative properties of beer. In this study, we used microsatellite markers to investigate genetic diversity and genetic differentiation of wild hop populations sampled in the northwestern part of Croatia. Analysis of 12 microsatellite loci revealed high diversity and weak population differentiation among wild hop populations. A total of 152 alleles were determined with an average of 12.67 alleles per locus. Observed heterozygosity ranged from 0.689 to 0.839 (average 0.767) and expected heterozygosity ranged from 0.725 to 0.789 (average 0.760). A total of 38 private alleles were detected. The data suggest that H. lupulus populations are not affected by recent bottlenecks. The degree of genetic differentiation among populations was low and not significant for most pairwise FST values, except for the pair of geographically most distant populations. The results did not indicate the existence of genetic structure among the sampled populations. The high genetic diversity and low differentiation among populations, combined with the absence of isolation by distance, indicate the existence of substantial gene flow among wild hop populations. Therefore, extensive sampling per population is clearly required to assess the genetic diversity of hop populations. Sampling strategies involving sampling across a large number of localities represented by only a few samples could lead to erroneous conclusions.
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Association between a genetic variant in scavenger receptor class B type 1 and its role on codon usage bias with increased risk of developing coronary artery disease. Clin Biochem 2021; 95:60-65. [PMID: 34097878 DOI: 10.1016/j.clinbiochem.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Coronary artery disease (CAD) as an important cause of morbidity and mortality globally. The scavenger receptor class B type 1 (SCARB1) plays an essential role in the reverse cholesterol transport. We have explored the association between a genetic variant, rs5888, in the SCARB1 gene with CAD and serum HDL-C levels. METHODS Patients were categorized into two groups' angiogram positive (>50% coronary stenosis) and angiogram negative (<50% coronary stenosis). Genotyping was carried out using polymerase chain reaction-amplification refractory mutation system. The association between the SNP rs5888 and serum HDL-C was analyzed using a logistic regression model. RESULTS The results showed that the subjects carrying a T allele was associated with a decreased serum HDL-C levels compared to the C allele in total population (p < 0.001). The risk of angiogram positivity in subjects carrying a T allele was 3.1-fold higher than for the control group (p < 0.001). CONCLUSION CVD patients carrying the T allele of rs5888 variant in the SCARB1 gene was associated with decreased serum level of HDL.
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Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution. Animals (Basel) 2021; 11:ani11051429. [PMID: 34067517 PMCID: PMC8156418 DOI: 10.3390/ani11051429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Habitat isolation and loss are significant factors that lead to the decline of wildlife populations worldwide, and habitat loss further leads to the shrinkage of populations, which increases the risk of inbreeding and the genetic decline of the populations. To explore the independent evolutionary characteristics of different populations, this study analyzed the genetic disparity of the introduced oriental fire-bellied toad in Beijing from a source population in Shandong Province. The results show that, despite originating from a small artificially introduced population, the toads in the Beijing region have maintained a moderate genetic diversity after 90 years of independent evolution, indicating that this species has a high capacity for survival and adaptation. Abstract Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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Prunier JG, Poesy C, Dubut V, Veyssière C, Loot G, Poulet N, Blanchet S. Quantifying the individual impact of artificial barriers in freshwaters: A standardized and absolute genetic index of fragmentation. Evol Appl 2020; 13:2566-2581. [PMID: 33294009 PMCID: PMC7691472 DOI: 10.1111/eva.13044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
Fragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized quantification of barrier effects. Indeed, observed levels of genetic differentiation GD depend on both the age of the obstacle and the effective size of the populations it separates, making comparisons of the actual barrier effect of different obstacles difficult. Here, we developed a standardized genetic index of fragmentation (F INDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The F INDEX is the standardized ratio between the observed GD between pairs of populations located on either side of an obstacle and the GD expected if this obstacle completely prevented gene flow. The expected GD is calculated from simulations taking into account two parameters: the number of generations since barrier creation and the expected heterozygosity of the populations, a proxy for effective population size. Using both simulated and empirical datasets, we explored the validity and the limits of the F INDEX. We demonstrated that it allows quantifying effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among obstacles of different ages and populations (or species) of different effective sizes. The F INDEX requires a minimum amount of fieldwork and genotypic data and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the F INDEX promising to support the management of freshwater species affected by barriers, notably for planning and evaluating restoration programs.
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Affiliation(s)
- Jérôme G. Prunier
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Camille Poesy
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
| | - Vincent Dubut
- CNRSIRDAvignon UniversitéIMBEAix Marseille UnivMarseille UniversitéFrance
| | - Charlotte Veyssière
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Géraldine Loot
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
| | - Nicolas Poulet
- DRAS, Pôle R&D écohydraulique OFBIMFT‐PPRIMEOffice Français de la BiodiversitéToulouseFrance
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS)Université Paul Sabatier (UPS)UMR 5321Station d’Ecologie Théorique et ExpérimentaleMoulisFrance
- CNRSUPSUMR 5174 EDB (Laboratoire Évolution & Diversité Biologique)École Nationale de Formation Agronomique (ENFA)Toulouse Cedex 4France
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Hadi S, Andayani N, Muttaqin E, Simeon BM, Ichsan M, Subhan B, Madduppa H. Genetic connectivity of the scalloped hammerhead shark Sphyrna lewini across Indonesia and the Western Indian Ocean. PLoS One 2020; 15:e0230763. [PMID: 33002022 PMCID: PMC7529310 DOI: 10.1371/journal.pone.0230763] [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: 03/06/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Scalloped Hammerhead shark (Sphyrna lewini) is an endangered species which its populations have been declining globally including in Indonesia, the world’s top shark fishing country. However, there is a lack of information on the recent population structure of this species to promote proper management and its conservation status. This study aimed to investigate the genetic diversity, population structure, and connectivity of the S. lewini population, in three major shark landing sites: Aceh (n = 41), Balikpapan (n = 30), and Lombok (n = 29). Meanwhile, additional sequences were retrieved from West Papua (n = 14) and the Western Indian Ocean (n = 65) populations. From the analyses of the mitochondrial CO1 gene, a total of 179 sequences of S. lewini, with an average size of 594 bp, and 40 polymorphic loci in four and eight haplotypes for the Indonesian population and the Western Indian Ocean population were identified. The overall values of genetic diversity were high (h = 0.717; π = 0.013), with the highest values recorded in Aceh (h = 0.668; π = 0.002) and the lowest in Papua (h = 0.143; π = 0.000). On the contrary, the overall value was fairly low in the Western Indian Ocean (h = 0.232; π = 0.001). Furthermore, AMOVA and FST showed three significant subdivisions in Indonesia (FST = 0.442; P < 0.001), with separated populations for Aceh and West Papua, and mixed between Balikpapan and Lombok (FST = 0.044; P = 0.091). In contrast, genetic homogeneity was observed within the population of the Western Indian Ocean (FST = –0.013; P = 0.612). The establishment of a haplotype network provided evidence of a significantly different population and a limited genetic distribution between the Indonesian and the Western Indian Ocean populations (FST = 0.740; P < 0.001). This study showed the presence of a complex population of S. lewini with limited connectivity only in Indonesia separated from the Western Indian Ocean and requiring specific management measures based on the population structure at the regional level.
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Affiliation(s)
- Sutanto Hadi
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
| | - Noviar Andayani
- Department of Biology, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Efin Muttaqin
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Benaya M. Simeon
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Muhammad Ichsan
- Wildlife Conservation Society Indonesia Program, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, Indonesia
- * E-mail:
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37
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Park HJ, Pichugin Y, Traulsen A. Why is cyclic dominance so rare? eLife 2020; 9:57857. [PMID: 32886604 PMCID: PMC7473768 DOI: 10.7554/elife.57857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/01/2020] [Indexed: 12/19/2022] Open
Abstract
Natural populations can contain multiple types of coexisting individuals. How does natural selection maintain such diversity within and across populations? A popular theoretical basis for the maintenance of diversity is cyclic dominance, illustrated by the rock-paper-scissor game. However, it appears difficult to find cyclic dominance in nature. Why is this the case? Focusing on continuously produced novel mutations, we theoretically addressed the rareness of cyclic dominance. We developed a model of an evolving population and studied the formation of cyclic dominance. Our results showed that the chance for cyclic dominance to emerge is lower when the newly introduced type is similar to existing types compared to the introduction of an unrelated type. This suggests that cyclic dominance is more likely to evolve through the assembly of unrelated types whereas it rarely evolves within a community of similar types.
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Affiliation(s)
- Hye Jin Park
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Asia Pacific Center for Theoretical Physics, Pohang, Republic of Korea
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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38
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von Takach B, Scheele BC, Moore H, Murphy BP, Banks SC. Patterns of niche contraction identify vital refuge areas for declining mammals. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13145] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
| | - Ben C. Scheele
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
- National Environmental Science Program Threatened Species Recovery Hub Australia
| | - Harry Moore
- School of Environmental Science Institute for Land, Water and Society Charles Sturt University Albury NSW Australia
| | - Brett P. Murphy
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
- National Environmental Science Program Threatened Species Recovery Hub Australia
| | - Sam C. Banks
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
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39
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Kyogoku D, Wheatcroft D. Heterospecific mating interactions as an interface between ecology and evolution. J Evol Biol 2020; 33:1330-1344. [PMID: 32762053 DOI: 10.1111/jeb.13687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/21/2020] [Indexed: 12/25/2022]
Abstract
Reproductive interference (costly interspecific sexual interactions) is well-understood to promote divergence in mating-relevant traits (i.e. reproductive character displacement: RCD), but it can also reduce population growth, eventually leading to local extinction of one of the species. The ecological and evolutionary processes driven by reproductive interference can interact with each other. These interactions are likely to influence whether the outcome is coexistence or extinction, but remain little studied. In this paper, we first develop an eco-evolutionary perspective on reproductive interference by integrating ecological and evolutionary processes in a common framework. We also present a simple model to demonstrate the eco-evolutionary dynamics of reproductive interference. We then identify a number of factors that are likely to influence the relative likelihoods of extinction or RCD. We discuss particularly relevant factors by classifying them into four categories: the nature of the traits responding to selection, the mechanisms determining the expression of these traits, mechanisms of reproductive interference and the ecological background. We highlight previously underappreciated ways in which these factors may influence the relative likelihoods of RCD and local extinction. By doing so, we also identify questions and future directions that will increase our holistic understanding of the outcomes of reproductive interference.
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40
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Ding XH, Hsu KC, Tang WQ, Liu D, Ju YM, Lin HD, Yang JQ. Genetic diversity and structure of the Chinese lake gudgeon ( Sarcocheilichthys sinensis). Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:228-237. [PMID: 32723222 DOI: 10.1080/24701394.2020.1779239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θ π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.
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Affiliation(s)
- Xin-Hua Ding
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Wen-Qiao Tang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yu-Min Ju
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan.,Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Hung-Du Lin
- Department of Biology, The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Jin-Quan Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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41
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Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Genetic variation across trophic levels: A test of the correlation between population size and genetic diversity in sympatric desert lizards. PLoS One 2019; 14:e0224040. [PMID: 31805058 PMCID: PMC6894812 DOI: 10.1371/journal.pone.0224040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/03/2019] [Indexed: 01/15/2023] Open
Abstract
Understanding the causes of genetic variation in real populations has been elusive. Competing theories claim that neutral vs. selective processes have a greater influence on the genetic variation within a population. A key difference among theories is the relationship between population size and genetic diversity. Our study tests this empirically by sampling two species of herbivorous lizards (Dipsosaurus dorsalis and Sauromalus ater) and two species of carnivorous lizards (Crotaphytus bicinctores and Gambelia wislizenii) that vary in population size at the same locality, and comparing metrics of genetic diversity. Contrary to neutral expectations, results from four independent loci showed levels of diversity were usually higher for species with smaller population sizes. This suggests that selective processes may be having an important impact on intraspecific diversity in this reptile community, although tests showed little evidence for selection on the loci sequenced for this study. It is also possible that idiosyncratic histories of the focal species may be overriding predictions from simple neutral models. If future studies show that lack of correlation between population size and genetic diversity is common, methods using genetic diversity to estimate population parameters like population size or time to common ancestor should be used with caution, as these estimates are based on neutral theory predictions.
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43
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Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island. Sci Rep 2019; 9:17997. [PMID: 31784623 PMCID: PMC6884562 DOI: 10.1038/s41598-019-54526-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/15/2019] [Indexed: 02/04/2023] Open
Abstract
How mating system impacts the genetic diversity of plants has long fascinated and puzzled evolutionary biologists. Numerous studies have shown that self-fertilising plants have less genetic diversity at both the population and species levels than outcrossers. However, the phylogenetic relationships between species and correlated ecological traits have not been accounted for in these previous studies. Here, we conduct a comparative population genetic study of two closely related selfing and outcrossing Zingiber species, with sympatric distribution in Hainan Island, and obtain a result contrary to previous studies. The results indicate that selfing Z. corallinum can maintain high genetic diversity through differentiation intensified by local adaptation in populations across the species’ range. In contrast, outcrossing Z. nudicarpum preserves high genetic diversity through gene exchange by frequent export of pollen within or among populations. Contrary to expectations, the major portion of genetic variation of outcrossing Z. nudicarpum may exist among populations, depending on the dispersal ability of pollen and seed. Our results also reveal that the main factor affecting population structure of selfing Z. corallinum is mountain ranges, followed by a moist climate, while that of outcrossing Z. nudicarpum is likely moisture, but not mountain ranges, due to gene flow via pollen.
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44
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Phukuntsi MA, Du Plessis M, Dalton DL, Jansen R, Cuozzo FP, Sauther ML, Kotze A. Population genetic structure of the thick-tailed bushbaby ( Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 31:1-10. [PMID: 31762360 DOI: 10.1080/24701394.2019.1694015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.
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Affiliation(s)
- Metlholo Andries Phukuntsi
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Environment, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Morne Du Plessis
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Biotechnology, University of Western Cape, Cape Town, South Africa
| | - Desiré Lee Dalton
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Raymond Jansen
- Department of Environment, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa
| | | | | | - Antoinette Kotze
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Genetics, University of the Free State, Bloemfontein, South Africa
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45
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Kvie KS, Heggenes J, Bårdsen BJ, Røed KH. Recent large-scale landscape changes, genetic drift and reintroductions characterize the genetic structure of Norwegian wild reindeer. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01225-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractLandscape changes, such as habitat loss and fragmentation, subdivide wild populations, reduce their size, and limit gene flow. These changes may further lead to depletion of genetic variation within populations as well as accelerating differentiation among populations. As a migratory species requiring large living areas, wild reindeer (Rangifer tarandus) is highly vulnerable to human activity. The number and continued presence of wild reindeer have been significantly reduced due to accelerating anthropogenic habitat modifications, as well as displacement in benefit of domesticated herds of the species. As a basis for future management strategies we assess genetic structure and levels of genetic variation in Norwegian wild reindeer by analysing 12 microsatellite loci and the mitochondrial control region in 21 management units with varying population sizes. Overall, both markers showed highly varying levels of genetic variation, with reduced variation in the smaller and more isolated populations. The microsatellite data indicated a relationship between population size and genetic variation. This relationship was positive and linear until a threshold for population size was reached at approximately 1500 reindeer. We found high levels of differentiation among most populations, indicating low levels of gene flow, but only a weak correlation between geographic and genetic distances. Our results imply that the genetic structure of Norwegian wild reindeer is mainly driven by recent colonization history, population size, as well as human-induced landscape fragmentation, restricting gene flow and leading to high levels of genetic drift. To sustain viable populations, conservation strategies should focus on genetic connectivity between populations.
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46
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Fuller N, Ford AT, Lerebours A, Gudkov DI, Nagorskaya LL, Smith JT. Chronic radiation exposure at Chernobyl shows no effect on genetic diversity in the freshwater crustacean, Asellus aquaticus thirty years on. Ecol Evol 2019; 9:10135-10144. [PMID: 31624541 PMCID: PMC6787803 DOI: 10.1002/ece3.5478] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome-wide SNP approach (Genotyping-by-sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping-by-sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation-by-Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome-wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long-term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.
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Affiliation(s)
- Neil Fuller
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Alex T. Ford
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Adélaïde Lerebours
- Institute of Marine Sciences, School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | - Dmitri I. Gudkov
- Department of Freshwater RadioecologyInstitute of HydrobiologyKievUkraine
| | - Liubov L. Nagorskaya
- Applied Science Center for Bioresources of the National Academy of Sciences of BelarusMinskBelarus
| | - Jim T. Smith
- School of Earth & Environmental SciencesUniversity of PortsmouthPortsmouthUK
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47
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Gajaweera C, Kang JM, Lee DH, Lee SH, Kim YK, Wijayananda HI, Kim JJ, Ha JH, Choi BH, Lee SH. Genetic diversity and population structure of the Sapsaree, a native Korean dog breed. BMC Genet 2019; 20:66. [PMID: 31382890 PMCID: PMC6683530 DOI: 10.1186/s12863-019-0757-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 06/20/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few decades. The aim of this study was to ascertain novel information about the genetic diversity, population structure, and demographic history of the Sapsaree breed using genome-wide single nucleotide polymorphism data. We characterized the genetic profile of the Sapsaree breed by comparison with seven foreign dog breeds with similar morphologies to estimate genetic differentiation within and among these breeds. RESULTS The results suggest that Sapsarees have higher genetic variance compared with the other breeds analyzed. The majority of the Sapsarees in this study share a discrete genetic pattern, although some individuals were slightly different, possibly as a consequence of the recent restoration process. Concordant results from analyses of linkage disequilibrium, effective population size, genetic diversity, and population structural analyses illustrate a relationship among the Sapsaree and the Tibetan breeds Tibetan terrier and Lhasa Apso, and a small genetic introgression from European breeds. The effective population size of the Sapsaree has contracted dramatically over the past generations, and is currently insufficient to maintain long-term viability of the breed's genetic diversity. CONCLUSIONS This study provides novel insights regarding the genetic diversity and population structure of the native Korean dog breed Sapsaree. Our results suggest the importance of a strategic and systematic approach to ensure the genetic diversity and the authenticity of the Sapsaree breed.
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Affiliation(s)
- Chandima Gajaweera
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
- Department of Animal Science, Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Ji Min Kang
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Doo Ho Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Soo Hyun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Yeong Kuk Kim
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hasini I. Wijayananda
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749 Republic of Korea
| | - Ji Hong Ha
- School of Life Science, Kyungpook National University, Daegu, 41940 Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Seung Hwan Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134 Republic of Korea
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48
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Takahashi R, Gushiken R, Nagata K, Shinzato A, Kantha SS, Yasuda M. Genetic Structure of the Ryukyu Wild Boar Population on Tokunoshima Island (Japan) Based on Modern and Ancient DNA Analyses: Evidence of Recent Gene Flow from Pigs to Wild Boars. MAMMAL STUDY 2019. [DOI: 10.3106/ms2018-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Ryohei Takahashi
- Department of Legal Medicine, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan
| | - Ryo Gushiken
- Board of Education Amagi Town, Hetono 2691-1, Amagi-cho, Oshima-gun, Kagoshima 891-7692, Japan
| | - Ken Nagata
- CrowLab Inc., Utsunomiya-ventures #3, Tochigi Prefecture Industrial Center, 3-1-4 Chuo, Utsunomiya-shi, Tochigi 320-0806, Japan
| | - Akito Shinzato
- Board of Education Isen Town, 2945-3 Isen, Isen-cho, Oshima-gun, Kagoshima 891-8201, Japan
| | - Sachi Sri Kantha
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Mirai Yasuda
- Board of Education Isen Town, 2945-3 Isen, Isen-cho, Oshima-gun, Kagoshima 891-8201, Japan
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49
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Grundler MR, Singhal S, Cowan MA, Rabosky DL. Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards. Mol Ecol 2019; 28:1664-1674. [PMID: 30739375 DOI: 10.1111/mec.15042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/01/2023]
Abstract
Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional-scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.
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Affiliation(s)
- Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, California
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,Department of Biology, CSU Dominguez Hills, Carson, California
| | - Mark A Cowan
- Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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50
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Gamboa M, Muranyi D, Kanmori S, Watanabe K. Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago. PLoS One 2019; 14:e0210269. [PMID: 30633758 PMCID: PMC6329508 DOI: 10.1371/journal.pone.0210269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - David Muranyi
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Deparment of Zoology, Plant Protection Institute Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Shota Kanmori
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
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