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Nagai K, Takahashi Y, Okabe H, Takahashi M, Tokita KI. Analysis of Genetic Structure and Genetic Diversity in Japanese Grey-Headed Lapwing Population Using mtDNA. Zoolog Sci 2024; 41:257-262. [PMID: 38809864 DOI: 10.2108/zs230094] [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: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 05/31/2024]
Abstract
The grey-headed lapwing (Vanellus cinereus) is a wading species in East Asia. However, examples of regional population dynamics and genetic research are limited. To reconsider the natural history and current status of the grey-headed lapwing in Japan, we analyzed the genetic diversity of the Japanese grey-headed lapwing population. We collected 77 grey-headed lapwing samples from 12 locations across Japan during the breeding season and three individuals during the wintering season and extracted DNA; 496-bp sequences of the ND2, which form part of the mitochondrial DNA, were determined for genetic analysis of the population. Consequently, 10 haplotypes were detected in 80 individuals, and 67 individuals, 84% of the total, shared two haplotypes, namely Vc1 and Vc2. Furthermore, the results showed that the prevalence of Vc1 was higher mainly in northern Japan, while that of Vc2 was higher mainly in southern Japan. Genetic diversity analysis showed that the overall haplotype diversity in Japan was 0.617, which is not particularly low. The sequence of Vc1 was exactly the same as that of grey-headed lapwing in China. Our study revealed the genetic structure of the grey-headed lapwing, suggesting that as the grey-headed lapwing expanded its distribution area into southern Japan, many Vc2-positive individuals migrated southward, resulting in a higher detection rate of Vc2 in southern Japan.
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Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan,
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
- Tohoku Natural History Research Group, Morioka, Iwate 020-8550, Japan
| | - Yusuke Takahashi
- Tohoku Natural History Research Group, Morioka, Iwate 020-8550, Japan
- Japan Wildlife Research Centre, Koto, Tokyo 130-8606, Japan
| | - Hiroto Okabe
- Kyushu Environmental Evaluation Association, Higashi-ku, Fukuoka-shi, Fukuoka 813-0004, Japan
| | - Masao Takahashi
- Iwate Prefectural Museum, Ueda, Morioka, Iwate 020-0102, Japan
| | - Ken-Ichi Tokita
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
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Khatun D, Tanaka T, Aranishi F. Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:10896-10910. [PMID: 38214853 DOI: 10.1007/s11356-023-31743-7] [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: 05/08/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.
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Affiliation(s)
- Dalia Khatun
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, 6808553, Japan
| | - Tomomi Tanaka
- Fisheries Ecosystem Project Center, Shimane University, Matsue, 6908504, Japan
| | - Futoshi Aranishi
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, 6808553, Japan.
- Fisheries Ecosystem Project Center, Shimane University, Matsue, 6908504, Japan.
- Institute of Agricultural and Life Sciences, Shimane University, Matsue, 6908504, Japan.
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Cryptic Lineage and Genetic Structure of Acanthopagrus pacificus Populations in a Natural World Heritage Site Revealed by Population Genetic Analysis. DIVERSITY 2022. [DOI: 10.3390/d14121117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent studies have revealed extensive genetic differentiation among some populations of marine taxa that were previously believed to be essentially homogeneous because larvae are widely dispersed in ocean currents. Acanthopagrus pacificus is a commercially and ecologically important teleost fish that is endemic to shallow coastal waters and estuaries of some tropical and sub-tropical areas in the West Pacific Ocean. Here, we examined genetic structure and the inferred demographic history of A. pacificus populations from mtDNA control region sequence data. A 677–678 base-pair fragment was sequenced from 159 individuals sampled at three localities across the West Pacific Ocean. Haplotype diversity was high, ranging from 0.915 to 0.989, while nucleotide diversity was low to medium, ranging from 0.8% to 2.60%. Analysis of molecular variance (AMOVA) showed significant genetic subdivision (FST = 0.155, p < 0.05) among sampled populations while pairwise FST estimates also revealed strong genetic differentiation among populations indicating that gene flow was restricted. Two distinct cryptic lineages were identified that were estimated to have diverged during the Pleistocene. In summary, contemporary factors including regional oceanic currents and self-recruitment are considered to have played significant roles in producing the population structure in this fish. In particular, the genetic information generated in the current study will allow appropriate fisheries management and conservation strategies to be developed for this important local fish in the waters around Iriomotejima Island, a World Heritage site.
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Panmictic stock structure of milkfish (Chanos chanos, Forsskål 1775) from Indian waters determined using mtDNA marker. J Genet 2022. [DOI: 10.1007/s12041-022-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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5
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Chow SW, Keshavmurthy S, Reimer JD, de Voogd N, Huang H, Wang JT, Tang SL, Schupp PJ, Tan CH, Liew HC, Soong K, Subhan B, Madduppa H, Chen CA. Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific. PeerJ 2022; 10:e13451. [PMID: 35669953 PMCID: PMC9165603 DOI: 10.7717/peerj.13451] [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: 06/23/2021] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise F ST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs.
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Affiliation(s)
- Savanna Wenhua Chow
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan,Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | | | - James Davis Reimer
- Department of Biology, Chemistry, and Marine Science, University of Ryukyus, Naha, Okinawa, Japan,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Nicole de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands,Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, Netherlands
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jih-Terng Wang
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany,Helmholtz Institute for Functional Marine Biodiversity at the, University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Chun Hong Tan
- School of Marine and Environmental Sceinces, University of Malaysia Terengganu, Terengganu, Malaysia
| | - Hock-Chark Liew
- Sdn Bhd. Jalan Hiliran, Kuala Terengganu, Alchemy Laboratory & Services, Terengganu, Malaysia
| | - Keryea Soong
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Beginer Subhan
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science & Technology, Faculty of Fisheries & Marine Sciences, IPB University, Bogor, Indonesia
| | - Chaolun Allen Chen
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan,Department of Life Science, Tunghai University, Taichung, Taiwan
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Nagai K, Tokita KI. Analysis of Genetic Structure and Genetic Diversity in Japanese Black Kite Population Using mtDNA. Zoolog Sci 2022; 39. [DOI: 10.2108/zs210121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/30/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Ken-ichi Tokita
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
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Fite T, Tefera T, Goftishu M, Damte T. Genetic diversity and demographic history of the Old World Bollworm,
Helicoverpa armigera
(Hubner) (Lepidoptera: Noctuidae), in Ethiopia inferred from mitochondrial gene sequences. Ecol Evol 2022; 12:e8907. [PMID: 35592065 PMCID: PMC9102519 DOI: 10.1002/ece3.8907] [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: 09/07/2021] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 11/05/2022] Open
Abstract
The Old World bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae), is a globally distributed agricultural and horticultural insect pest. Despite the economic importance of this insect in Ethiopia, its genetic diversity and demographic history are poorly understood. We examined the nucleotide variation of the mitochondrial cytochrome c oxidase subunit I (COI) gene fragment of 74 H. armigera individuals from six collection sites in Ethiopia. We recorded 15 COI haplotypes in H. armigera, ten globally shared and five exclusive to Ethiopia (HaET15, HaET14, HaET10, HaET7, and HaET4). Haplotype HaET1 was the most widely geographically distributed and frequent (71.62%). Analysis of molecular variance (AMOVA) revealed a high and significant level of variation within H. armigera populations (θST = −0.0135). Negative values of the neutrality test and nonsignificant index of mismatch distribution supported the demographic expansion of H. armigera populations in Ethiopia; furthermore, this was also supported by the nonsignificant values of the sum of squared deviations (SSD) and raggedness index (r). The high genetic variation and population expansion of H. armigera have immense implications for devising locally adapted management strategies in area‐wide integrated pest management IPM programs. However, a comprehensive study of H. armigera genetic diversity and population structure using various molecular markers is needed for future confirmation.
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Affiliation(s)
- Tarekegn Fite
- International Centre of Insect Physiology and Ecology (ICIPE) Addis Ababa Ethiopia
- School of Plant Sciences College of Agriculture and Environmental Sciences Haramaya University Dire Dhawa Ethiopia
| | - Tadele Tefera
- International Centre of Insect Physiology and Ecology (ICIPE) Addis Ababa Ethiopia
| | - Muluken Goftishu
- School of Plant Sciences College of Agriculture and Environmental Sciences Haramaya University Dire Dhawa Ethiopia
| | - Tebekew Damte
- Debre Zeit Agricultural Research Center Pulses, Oil and Fibre Crops Research Team Ethiopian Institute of Agricultural Research Debre Zeit Oromiya Ethiopia
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Schwarz S, Roe KJ. Population structure and gene flow in the Sheepnose mussel (
Plethobasus cyphyus
) and their implications for conservation. Ecol Evol 2022; 12:e8630. [PMID: 35222980 PMCID: PMC8854780 DOI: 10.1002/ece3.8630] [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: 07/15/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 11/07/2022] Open
Abstract
North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (Plethobasus cyphyus). Population structure analyses reveal five populations, three in the Upper Mississippi River Basin and two in the Ohio River Basin. Sampling locations exhibit a high degree of genetic diversity and contemporary migration estimates indicate that migration within river basins is occurring, although at low rates, but there is no migration is occurring between the Ohio and Mississippi river basins. No evidence of bottlenecks was detected, and almost all locations exhibited the signature of population expansion. Our results indicate that although anthropogenic activity has altered the landscape across the range of the Sheepnose, these activities have yet to be reflected in losses of genetic diversity. Efforts to conserve Sheepnose populations should focus on maintaining existing habitats and fostering genetic connectivity between extant demes to conserve remaining genetic diversity for future viable populations.
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Affiliation(s)
- Sara Schwarz
- Department of Natural Resources Ecology and Management Iowa State University Ames Iowa USA
- Ecology and Evolutionary Biology Program Iowa State University Ames Iowa USA
| | - Kevin J. Roe
- Department of Natural Resources Ecology and Management Iowa State University Ames Iowa USA
- Ecology and Evolutionary Biology Program Iowa State University Ames Iowa USA
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Lin HC, Tsai CJ, Wang HY. Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes. PeerJ 2022; 9:e12639. [PMID: 35003932 PMCID: PMC8684317 DOI: 10.7717/peerj.12639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22-39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age. Main conclusions The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.
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Affiliation(s)
- Hsiu-Chin Lin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chia-Jung Tsai
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hui-Yu Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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10
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Cárcamo-Tejer V, Vila I, Llanquín-Rosas F, Sáez-Arteaga A, Guerrero-Jiménez C. Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish. PeerJ 2021; 9:e11917. [PMID: 34484986 DOI: 10.7717/peerj.11917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/15/2021] [Indexed: 11/20/2022] Open
Abstract
From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
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Affiliation(s)
- Violeta Cárcamo-Tejer
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Francisco Llanquín-Rosas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Alberto Sáez-Arteaga
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
| | - Claudia Guerrero-Jiménez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
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Cortez T, Amaral RV, Sobral-Souza T, Andrade SCS. Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Rafael V Amaral
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, MTBrazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
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12
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Liu HL, Chen ZT, Liu C, Wu XL, Xiao KJ, Pu DQ. Population Genetics of the Black Citrus Aphid Aphis aurantii (Hemiptera, Aphididae) in China. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.702178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The black citrus aphid, Aphis aurantiiBoyer de Fonscolombe, 1841, is one of the most destructive pests in commercial tea plantations and gardens in China. In this study, we investigated the population genetic structure of A. aurantii based on the concatenated sequences of two mitochondrial genes, cytochrome c oxidase I (cox1) and cytochrome b (cytb). A total of 166 haplotypes were identified from 177 individuals collected at 11 locations in China. The whole Chinese A. aurantii population showed a low nucleotide diversity (0.00968) and a high population diversity (haplotype diversity; 0.9991). The haplotypes of the 11 local populations were widely distributed in the neighbor-joining phylogenetic tree and haplotype network diagram, whereas no apparent lineages were detected. Gene flow analysis showed gene exchanges among local populations. The pairwise Fst values revealed a certain amount of genetic difference among local populations. Analysis of molecular variance (AMOVA) reflected genetic differences both within and among populations. The isolation by distance (IBD) analysis revealed a high positive correlation between the geographic distance and genetic distance of the different populations. Neutral test and mismatch distribution suggested that A. aurantii may have experienced recent population expansion events.
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Still time for action: genetic conservation of imperiled South Canadian River fishes, Arkansas River Shiner (Notropis girardi), Peppered Chub (Macrhybopsis tetranema) and Plains Minnow (Hybognathus placitus). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01374-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Drahun I, Wiebe KF, Koloski CW, van Herk WG, Cassone BJ. Genetic structure and population demographics of Hypnoidus bicolor (Coleoptera: Elateridae) in the Canadian Prairies. PEST MANAGEMENT SCIENCE 2021; 77:2282-2291. [PMID: 33421259 DOI: 10.1002/ps.6255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Following banning of the pesticide lindane in most counties, wireworms (i.e., the soil-living larval stages of click beetles) have become major pests of a variety of economically important field crops. Hypnoidus bicolor is a common pest species in the Canadian Prairies. However, little is known about its life history, which impedes the development of effective integrated pest management (IPM) strategies. Population genetic approaches have the potential to assist in the development of IPM. RESULTS We sequenced a 622-bp fragment of the COX1 gene from 326 H. bicolor wireworm and click beetles collected from 13 localities on the Canadian Prairies. Two genetically distinct (>4.66% sequence divergence) clades were identified, suggesting that they may be part of a species complex. Clade A predominated and increased in prevalence the further east samples were collected, whereas the opposite was true for clade B. Clade B appears to be comprised of two mitochondrial DNA groups, however, one group was represented by only one haplotype. Both clades were characterized by uneven gene flow among populations with low levels of regional genetic structuring. Clade A appeared to have undergone population and range expansions, which may coincide with the advent of intensive agriculture practices in the prairies. CONCLUSION Knowledge of species composition and population structure is important for the development of effective IPM strategies but is often lacking for wireworms. Our study fills these knowledge gaps for a predominant pest species in the prairies, H. bicolor, by providing robust evidence for cryptic forms and characterizing its dispersal patterns and population dynamics. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Ivan Drahun
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Kiana F Wiebe
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Cody W Koloski
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Willem G van Herk
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, British Columbia, Canada
| | - Bryan J Cassone
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
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Cambrone C, Cézilly F, Wattier R, Eraud C, Bezault E. Levels of genetic differentiation and gene flow between four populations of the Scaly-naped Pigeon, Patagioenas squamosa: implications for conservation. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2021. [DOI: 10.1080/01650521.2021.1878765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Christopher Cambrone
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
| | - Frank Cézilly
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
- Université d’Etat d’Haïti, Port-au-Prince, Haiti
| | - Rémi Wattier
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Cyril Eraud
- Office Français de la Biodiversité, Unité Avifaune Migratrice, Chizé, France
| | - Etienne Bezault
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
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17
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Nagai K, Manawatthana S, Tokita KI, Nualsri C, Pierce AJ, Sutasha K, Sribuarod K, Takehara K, Round PD, Higuchi H. Genetic Structure in Japanese and Thai Populations of the Japanese Sparrowhawk Accipiter gularis. Zoolog Sci 2020; 37:232-239. [PMID: 32549537 DOI: 10.2108/zs190104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/15/2020] [Indexed: 11/17/2022]
Abstract
The Japanese sparrowhawk Accipiter gularis is a small raptor that breeds in Northeast Asia. The species consists of the widespread and mostly migratory subspecies A. g. gularis that is common in East Asia, including Japan, and the resident and endangered subspecies A. g. iwasakii which inhabits the Ryukyu and Yaeyama Islands in Okinawa, southern Japan. Given the minimal knowledge about the migration of the species, in this study we sought to compare the genetic variation of the populations breeding in Japan with those migrating through Southeast Asia. We sequenced 761 bp of mitochondrial DNA Control Region from each of 21 A. gularis collected during the breeding season in Japan and from 20 individuals intercepted on migration in Thailand. We detected 26 haplotypes among the 41 individuals which differed significantly between Japan and Thailand. Migrants in Thailand were presumed to have originated from a wide area in Eastern Eurasia. The phylogenetic and network analyses demonstrated that the haplotypes of all A. g. gularis detected in Japan were genetically close. Moreover, the Okinawa haplotypes of A. g. iwasakii were clustered with moderate genetic variation. The information presented here can be used towards implementing future conservation actions.
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Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan,
| | - Sontaya Manawatthana
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Ken-Ichi Tokita
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
| | - Chukiat Nualsri
- Monnang Subdistrict Municipality, Monnang, Phanat Nikhom, Chonburi 20140, Thailand
| | - Andrew J Pierce
- Conservation Ecology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkhunthien, Bangkok 10150, Thailand
| | - Kaset Sutasha
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Kriangsak Sribuarod
- Khlong Saeng Wildlife Research Station, Department of National Parks, Wildlife and Plants Conservation, Khao Phang, Ban Tha Khun, Surat Thani 84230, Thailand
| | | | - Philip D Round
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Hiroyoshi Higuchi
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan
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18
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Kafaei S, Sharifi M, Akmali V. Population Genetic Structure and Phylogeography of the Small Mouse-Tailed Bat, Rhinopoma muscatellum Thomas, 1903 (Chiroptera: Rhinopomatidae) in Iran Inferred from Mitochondrial DNA. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.1.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sasan Kafaei
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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19
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Ruiz-García M, Arias Vásquez JY, Restrepo H, Cáceres-Martínez CH, Shostell JM. The genetic structure of the spectacled bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa082] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AbstractThe spectacled bear (Ursidae: Tremarctos ornatus) is an emblematic umbrella species and one of the top carnivores in the Andean mountains. It is also listed as vulnerable by IUCN and as endangered by CITES. We analyzed the genetic structure of this species in nine geographical regions representing the three Andean Cordilleras in Colombia. We sequenced six mitochondrial genes in 115 spectacled bears; a subset of these specimens (n = 61) were genotyped at seven nuclear microsatellites. We addressed three objectives: 1) determine the genetic diversity and historical demographic changes of the spectacled bear in Colombia; 2) determine phylogeographic patterns of genetic divergence among spectacled bear populations in Colombia; and 3) estimate the levels of gene flow among different regions of Colombia. Our analyses show evidence of high mitochondrial genetic diversity in spectacled bears, both in Colombia as well as in each of the nine regions, most particularly Norte de Santander, Nariño, and Antioquia-Córdoba. In addition, we detected population expansion in Colombia that occurred around 24,000 years ago, followed by a population decrease during the last 7,000 years, and a sudden expansion in the last 300 years. Phylogenetic analyses showed few well-supported clades, with some haplotypes detected in all the departments and Colombian Andean Cordilleras, and other haplotypes restricted to certain geographical areas (Antioquia, Norte de Santander, Cundinamarca, and Nariño). We detected significant genetic heterogeneity among some departments and among the three Colombian Andean Cordilleras for both mitochondrial and nuclear genes. Nevertheless, the moderate levels of gene flow estimated from FST statistics suggest that geographical barriers have not been definitive obstacles to the dispersion of the spectacled bear throughout Colombia. Despite these gene flow estimates, significant spatial autocorrelation was detected for spectacled bear in Colombia, where two kinds of spatial patterns were discovered: genetic patches of 144 km of diameter, and isolation by distance among bears separated from 578 to 800 km. The two most northern spectacled bear populations of Colombia (Norte de Santander and Antioquia) also were the two most differentiated. Their distinctiveness may qualify them as distinct Management Units (MUs) in the context of conservation policies for the spectacled bear in Colombia.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - Jessica Yanina Arias Vásquez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | | | - Carlos Herney Cáceres-Martínez
- Grupo de Investigación en Ecología y Conservación de Fauna Silvestre, Universidad Nacional de Colombia, sede Medellín, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
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20
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Divya PR, Jency PME, Joy L, Kathirvelpandian A, Singh RK, Basheer VS. Population connectivity and genetic structure of Asian green mussel, Perna viridis along Indian waters assessed using mitochondrial markers. Mol Biol Rep 2020; 47:5061-5072. [PMID: 32524388 DOI: 10.1007/s11033-020-05575-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/05/2020] [Indexed: 11/24/2022]
Abstract
Perna viridis (Linnaeus, 1758), the Asian green mussel, belonging to the family Mytilidae is widely distributed along the Indian coast. The species is majorly found in southeastern countries and is considered an ideal candidate for aquaculture due to its high nutritional value and growth rate. Obtaining their genetic information is essential for their sustainable capture-based production. In the present study, genetic variation, population structure, and demographic processes of the populations across the distribution of this species were assessed using the mitochondrial DNA ATPase6 and cytb gene. In total, we selected 170 samples from five localities across the Indian subcontinent including Andaman Sea. Sequence analysis of partial cytb (885 bp) and ATPase6 (714 bp) genes revealed 45 and 58 haplotypes, respectively. The significant coefficient of genetic differentiation (FST: 0.255 for cytb and 0.252 for ATPase6) and analyses of molecular variance indicated three varieties of stocks, namely Arabian Sea, Bay of Bengal, and Andaman Sea. All the populations showed low nucleotide diversity, suggesting severe historical bottleneck events and high haplotype diversity, indicating population expansion. The genetic variation and demographic process reported in this study will form the baseline information for framing policies, which can be adopted while planning stock specific ranching and relaying programmes in the Indian subcontinent with view to enhance and manage the fishery.
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Affiliation(s)
- P R Divya
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India.
| | - P M Elizabeth Jency
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - Linu Joy
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - A Kathirvelpandian
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
| | - Rajeev Kumar Singh
- ICAR National Bureau of Fish Genetic Resources, Dilkusha Post, Canal ring Road, Lucknow, 226002, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources Centre, ICAR NBFGR, CMFRI Campus, Cochin, Kerala, 682018, India
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21
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Ruiz-Arce R, Todd TN, Deleon R, Barr NB, Virgilio M, De Meyer M, McPheron BA. Worldwide Phylogeography of Ceratitis capitata (Diptera: Tephritidae) Using Mitochondrial DNA. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1455-1470. [PMID: 32112108 DOI: 10.1093/jee/toaa024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 06/10/2023]
Abstract
The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is one of the most economically important tephritid species worldwide. It has spread across six geographic regions as a result of successful invasions and continues to cause substantial losses to agricultural communities. Our study examined 1,864 flies originating from 150 localities, using mitochondrial DNA sequencing methods. We tested for population structure and revealed the genetic diversity for 1,592 specimens gathered from 144 wild fly collections from 46 countries representing the entire geographic range for this species. We also include in this study 272 Sterile Insect Technique (SIT) specimens from four SIT facilities. We recovered 202 haplotypes from the current sampling and updated previously published work to reveal a total of 231 haplotypes for this pest. These data show population structure at and below the regional level for these collections, shedding light on the current demographics for this species. We observed four common haplotypes, seen among 62% of the samples sequenced that have worldwide distribution. Three haplotypes were seen in SIT flies, with one seen as the predominant haplotype. Our work showed that two of the haplotypes were private to SIT flies, not present among wild fly collections. However, a third haplotype common among wild fly collections was also seen in one SIT facility but at a low frequency based on the current sampling. We provide guidance on the interpretation of these methods for the source estimation of current and future infestations.
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Affiliation(s)
| | | | | | | | | | | | - Bruce A McPheron
- Department of Entomology, The Pennsylvania State University, University Park, PA
- The Ohio State University, Columbus, OH
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22
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Campos E, Cuéllar J, Salvador O, García-Trejo EA, Pereira F. The genetic diversity and phylogeography of Mexican domestic sheep. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106109] [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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23
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Ruiz-García M, Castellanos A, Arias-Vásquez JY, Shostell JM. Genetics of the Andean bear ( Tremarctos ornatus; Ursidae, Carnivora) in Ecuador: when the Andean Cordilleras are not an Obstacle. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:190-208. [PMID: 32468901 DOI: 10.1080/24701394.2020.1769088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
One of the top carnivores in the Andean mountains is the Andean bear (Tremarctos ornatus, Ursidae), the only bear in South America. This is a flagship and key umbrella species in Ecuador because its conservation has a positive impact on the conservation of many other species in the Andes. But to preserve, first one must know the genetic characteristics of a species, among other things. For this, we analyzed six mitochondrial genes and seven nuclear DNA microsatellites of 108 Andean bear specimens sampled throughout Ecuador. We adopted three strategies for analyzing the data: by Province, by Region (north vs south), and by Cordillera. Four main results were obtained. First, the mitochondrial genetic diversity levels were elevated, but there were no differences in genetic diversity by Province or by Cordillera. By Regions, southern Ecuador had higher genetic diversity levels than to northern Ecuador. The genetic diversity for the microsatellites was only medium for the Andean bear at this country. Second, there was clear and significant evidence of female population expansions, for the overall sample, by Province, Region, and Cordillera. This population expansion was determined to have occurred in the time interval of 30,000-20,000 years ago (YA), during the last phase of the Pleistocene. We detected a population decrease to have occurred more recently, within the last 5000 years. It continued until about 300-200 YA when a population increase was again detected. Third, there were, practically, no phylogeographic pattern nor genetic differentiation among Andean bear populations in Ecuador by Province or by Cordillera for either mitochondrial or microsatellite markers. There was a little more genetic differentiation between northern and southern areas. Fourth, there was no trace of significant spatial genetic structure for the Andean bear in Ecuador in agreement with the genetic differentiation analyses. This shows that the Andean Cordilleras in this country did not present an obstacle to the dispersion of this species. Therefore, all of the Andean bear specimens in Ecuador should be treated as a unique Management Unit (MU) for conservation purposes, differently to that determined for other countries as Colombia.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Armando Castellanos
- Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador.,Andean Bear Foundation, Quito, Ecuador
| | - Jessica Yanina Arias-Vásquez
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
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24
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Rojo JH, Fernández DA, Figueroa DE, Boy CC. Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus. JOURNAL OF FISH BIOLOGY 2020; 96:956-967. [PMID: 32048294 DOI: 10.1111/jfb.14285] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/04/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
This study reports the phenotypic and genetic differences between individuals of puyen Galaxias maculatus from two sites in the same river basin in Tierra del Fuego National Park, southern South America. Individuals from the two sampling sites presented morphometric and genetic differences. The morphometric differences indicated that individuals from Laguna Negra (LN) were short and more robust and had large eyes, whereas those from Arroyo Negro (AN) were thin and elongated and had small eyes. Genetic differences showed that AN individuals had a greater genetic structuration and an older demographic history than LN individuals. The results of this study affirmed that the individuals from the two sampling sites belong to different populations with a high degree of isolation. The demographic history could indicate that the individuals of G. maculatus which migrated to northern areas during the last glaciation settled in the Beagle Channel after its formation. The LN population could have originated after the retreat of the glaciers, migrating from AN.
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Affiliation(s)
- Javier Hernán Rojo
- Centro Austral de Investigaciones Científicas (CADIC) - CONICET, Ushuaia, Argentina
| | - Daniel Alfredo Fernández
- Centro Austral de Investigaciones Científicas (CADIC) - CONICET, Ushuaia, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales de la Universidad Nacional de Tierra del Fuego (ICPA-UNTDF), Ushuaia, Argentina
| | - Daniel Enrique Figueroa
- Instituto de Investigaciones Marinas y Costeras (IIMyC) - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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Chanthran SSD, Lim PE, Li Y, Liao TY, Poong SW, Du J, Hussein MAS, Sade A, Rumpet R, Loh KH. Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. Zookeys 2020; 911:139-160. [PMID: 32104142 PMCID: PMC7031388 DOI: 10.3897/zookeys.911.39222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 11/22/2022] Open
Abstract
A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167-0.9952, low nucleotide diversity ranging from 0.0288-0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.
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Affiliation(s)
- Shyama Sundari Devi Chanthran
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
- Institute for Advanced Studies, University of Malaya, Kuala Lumpur 50603, MalaysiaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
| | - Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaNational Sun Yat-sen UniversityKaohsiungTaiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, TaiwanMinistry of Natural ResourcesXiamenChina
| | - Sze-Wan Poong
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
| | - Jianguo Du
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaNational Sun Yat-sen UniversityKaohsiungTaiwan
- Fujian Provincial Station for Field Observation and Research of Island and Coastal Zone in Zhangzhou, Xiamen 361005, ChinaStation for Field Observation and Research of Island and Coastal ZoneXiamenChina
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, ChinaKey Laboratory of Marine Ecological Conservation and RestorationXiamenChina
| | - Muhammad Ali Syed Hussein
- Endangered Marine Species Research Unit, Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, MalaysiaUniversiti Malaysia SabahKota KinabaluMalaysia
| | - Ahemad Sade
- Department of Fisheries Sabah, Kota Kinabalu 88624, Sabah, MalaysiaDepartment of Fisheries SabahKota KinabaluMalaysia
| | - Richard Rumpet
- Fisheries Research Institute, Sarawak, Department of Fisheries Malaysia, Kuching 93744, Sarawak, MalaysiaDepartment of Fisheries MalaysiaKuchingMalaysia
| | - Kar-Hoe Loh
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
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26
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Mkize LS, Zishiri OT. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Trop Anim Health Prod 2020; 52:2079-2089. [PMID: 32048149 DOI: 10.1007/s11250-020-02231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise FST = 0.066 and Slatkins FST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.
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Affiliation(s)
| | - Oliver Tendayi Zishiri
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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27
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Veith M, Göçmen B, Sotiropoulos K, Eleftherakos K, Lötters S, Godmann O, Karış M, Oğuz A, Ehl S. Phylogeographic analyses point to long-term survival on the spot in micro-endemic Lycian salamanders. PLoS One 2020; 15:e0226326. [PMID: 31929551 PMCID: PMC6957296 DOI: 10.1371/journal.pone.0226326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/25/2019] [Indexed: 11/18/2022] Open
Abstract
Lycian salamanders (genus Lyciasalamandra) constitute an exceptional case of micro-endemism of an amphibian species on the Asian Minor mainland. These viviparous salamanders are confined to karstic limestone formations along the southern Anatolian coast and some islands. We here study the genetic differentiation within and among 118 populations of all seven Lyciasalamandra species across the entire genus’ distribution. Based on circa 900 base pairs of fragments of the mitochondrial 16SrDNA and ATPase genes, we analysed the spatial haplotype distribution as well as the genetic structure and demographic history of populations. We used 253 geo-referenced populations and CHELSA climate data to infer species distribution models which we projected on climatic conditions of the Last Glacial Maximum (LGM). Within all but one species, distinct phyloclades were identified, which only in parts matched current taxonomy. Most haplotypes (78%) were private to single populations. Sometimes population genetic parameters showed contradicting results, although in several cases they indicated recent population expansion of phyloclades. Climatic suitability of localities currently inhabited by salamanders was significantly lower during the LGM compared to recent climate. All data indicated a strong degree of isolation among Lyciasalamandra populations, even within phyloclades. Given the sometimes high degree of haplotype differentiation between adjacent populations, they must have survived periods of deteriorated climates during the Quaternary on the spot. However, the alternative explanation of male biased dispersal combined with a pronounced female philopatry can only be excluded if independent nuclear data confirm this result.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
- * E-mail:
| | - Bayram Göçmen
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | | | - Karolos Eleftherakos
- Section of Zoology-Marine Biology, Department of Biology, University of Athens, Athens, Greece
| | - Stefan Lötters
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
| | | | - Mert Karış
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | - Anil Oğuz
- Ege University, Faculty of Science, Department of Biology, Zoology Section, Bornova, İzmir, Turkey
| | - Sarah Ehl
- Department of Biogeography, Trier University, Universitätsring, Trier, Germany
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Nagai K, Nakayama F, Tokita KI, Kawakami K. Genetic Structure and Diversity of Two Populations of the Eastern Buzzard ( Buteo japonicus japonicus and B. j. toyoshimai) in Japan. Zoolog Sci 2020; 36:471-478. [PMID: 31833318 DOI: 10.2108/zs190030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
The nominotypical subspecies of the Eastern buzzard (Buteo japonicus japonicus; BJJ) is a common raptor inhabiting East Asia and Japan. Another subspecies, B. j. toyoshimai (BJT), inhabits only the Bonin Islands of the Ogasawara Islands, where there are only an estimated 85 breeding pairs. Because of this low population size, this subspecies is classified as endangered (class IB) in Japan. The aims of the present study were to examine genetic differences between BJJ and BJT, determine the genetic structure of the Eastern Buzzard, and assess genetic diversity within each subspecies. We sequenced 1526 bp within the control region of the mtDNA of 10 BJJ individuals during the breeding season in four sites; similarly, we sequenced 23 BJJ individuals during winter in three sites. We detected 24 haplotypes among the 33 individuals. In a similar analysis performed with 12 BJT individuals, three haplotypes were detected. The phylogenetic analysis showed that BJJ and BJT have diverged into distinct clades, supporting the genetic differentiation between the subspecies. Network and mismatch distribution analyses indicated that BJJ may have experienced population expansion. In addition, comparisons with other raptors revealed a high degree of genetic diversity in the BJJ population. In contrast, the genetic diversity of the BJT population is lower than that in other raptors. Our results indicated that it is necessary to protect BJT to prevent the reduction in its genetic diversity.
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Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan,
| | | | - Ken-Ichi Tokita
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Kazuto Kawakami
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
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Kramer KL. How There Got to Be So Many of Us: The Evolutionary Story of Population Growth and a Life History of Cooperation. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2019. [DOI: 10.1086/705943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nakamura Y, Yamagishi J, Hayashida K, Osada N, Chatanga E, Mweempwa C, Chilongo K, Chisi J, Musaya J, Inoue N, Namangala B, Sugimoto C. Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi. PLoS Negl Trop Dis 2019; 13:e0007568. [PMID: 31344039 PMCID: PMC6657825 DOI: 10.1371/journal.pntd.0007568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/21/2019] [Indexed: 12/23/2022] Open
Abstract
The tsetse fly, Glossina morsitans morsitans, is a significant problem in Zambia and Malawi. It is the vector for the human infective parasite Trypanosoma brucei rhodesiense, which causes human African trypanosomiasis, and various Trypanosoma species, which cause African animal trypanosomiasis. Understanding the genetic diversity and population structure of G. m. morsitans is the basis of elucidating the connectivity of the tsetse fly populations, information that is essential in implementing successful tsetse fly control activities. This study conducted a population genetic study using partial mitochondrial cytochrome oxidase gene 1 (CO1) and 10 microsatellite loci to investigate the genetic diversity and population structure of G. m. morsitans captured in the major HAT foci in Zambia and Malawi. We have included 108 and 99 G. m. morsitans samples for CO1 and microsatellite analyses respectively. Our results suggest the presence of two different genetic clusters of G. m. morsitans, existing East and West of the escarpment of the Great Rift Valley. We have also revealed genetic similarity between the G. m. morsitans in Kasungu National Park and those in the Luangwa river basin in Zambia, indicating that this population should also be included in this historical tsetse belt. Although further investigation is necessary to illustrate the whole picture in East and Southern Africa, this study has extended our knowledge of the population structure of G. m. morsitans in Southern Africa. Techniques from population genetics have been widely applied to assess problems in evolutionary biology, computational biology, wildlife conservation, animal breeding, etc. In this study, we used population genetics approaches to elucidate the genetic population structure of the tsetse fly Glossina morsitans morsitans, an important vector of the Trypanosoma parasite. Our aim was to identify the optimal range of areas in which to implement effective tsetse fly control programs. We focused on five areas of active human African trypanosomiasis foci in Zambia and Malawi and used both mitochondrial and nuclear markers for population genetics analyses. High levels of genetic differentiation were observed between G. m. morsitans in Nkhotakota Wildlife Reserve, Malawi, and those at the other locations included in this study. Nkhotakota Wildlife Reserve lies on the eastern side of the escarpment of the Great Rift Valley at an altitude that is at the biological limit of G. m. morsitans, thereby functioning as a geographical barrier restricting gene flow from the G. m. morsitans on the western side of the escarpment. The western side of the escarpment is part of a historically-known tsetse belt that resides within the Luangwa river basin. We have demonstrated that a previously undescribed population of G. m. morsitans in Kasungu National Park, Malawi, should be included in this historical tsetse belt.
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Affiliation(s)
- Yukiko Nakamura
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail: (YN); (JY)
| | - Junya Yamagishi
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Station for Zoonosis Control, GI-CORE, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail: (YN); (JY)
| | - Kyoko Hayashida
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Elisha Chatanga
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Veterinary Medicine, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Cornelius Mweempwa
- Department of Veterinary Services, Tsetse and Trypanosomiasis Control Unit, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Kalinga Chilongo
- Department of Veterinary Services, Tsetse and Trypanosomiasis Control Unit, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - John Chisi
- Department of Basic Medical Science, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Janelisa Musaya
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Noboru Inoue
- Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido, Japan
| | - Boniface Namangala
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Station for Zoonosis Control, GI-CORE, Hokkaido University, Sapporo, Hokkaido, Japan
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Ericson PGP, Qu Y, Rasmussen PC, Blom MPK, Rheindt FE, Irestedt M. Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. BMC Evol Biol 2019; 19:151. [PMID: 31340765 PMCID: PMC6657069 DOI: 10.1186/s12862-019-1481-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
Background Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. Results We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. Conclusions We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, “stepping-stone” dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea. Electronic supplementary material The online version of this article (10.1186/s12862-019-1481-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pamela C Rasmussen
- Department of Integrative Biology and MSU Museum, Michigan State University, East Lansing, 48824, MI, USA.,Bird Group, The Natural History Museum, Akeman Street, Tring, HP23 6AP, UK
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 119077, Singapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
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Andersen LW, Dirksen R, Nikulina EA, Baagøe HJ, Petersons G, Estók P, Orlov OL, Orlova MV, Gloza‐Rausch F, Göttsche M, Fjederholt ET, Krüger F, Elmeros M. Conservation genetics of the pond bat ( Myotis dasycneme) with special focus on the populations in northwestern Germany and in Jutland, Denmark. Ecol Evol 2019; 9:5292-5308. [PMID: 31110680 PMCID: PMC6509384 DOI: 10.1002/ece3.5119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/07/2022] Open
Abstract
Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as "Near Threatened" with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary, and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany, and Russia were analyzed at 10 microsatellite loci; 241 samples representing all areas were analyzed using mitochondrial D-loop and cytochrome B sequences. A Bayesian clustering approach revealed two poorly resolved clusters, one representing the Danish and German groups and the other the Russian group. However, significantly different pairwise F ST and D EST estimates were observed between the Danish and German groups and between the Danish and Russian groups suggesting a recent population structure. These conflicting results might be attributed to the effect of migration or low resolution due to the number of microsatellite markers used. After concatenating the two mitochondrial sequences, analysis detected significant genetic differentiation between all populations, probably due to genetic drift combined with a founder event. The phylogenetic tree suggested a closer relationship between the Russian and Northern European populations compared to the Hungarian population, implying that the latter belongs to an older ancestral population. This was supported by the observed haplotype network and higher nucleotide diversity in this population. The genetic structuring observed in the Danish/German pond bat stresses the need for a cross-border management between the two countries. Further, the pronounced mtDNA structuring, together with the indicated migration between nearby populations suggest philopatric female behavior but male migration, emphasizes the importance of protecting suitable habitat mosaics to maintain a continuum of patches with dense pond bat populations across the species' distribution range.
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Affiliation(s)
| | - Ronja Dirksen
- Population Genetics Group, Department of Biology, Zoological InstituteChristian‐Albrechts University of KielKielGermany
| | - Elena A. Nikulina
- Centre for Baltic and Scandinavian Archaeology (ZBSA)Schleswig‐Holstein State Museums FoundationSchleswigGermany
| | | | - Gunars Petersons
- Faculty of Veterinary MedicineLatvia University of Life Sciences and TechnologiesJelgavaLatvia
| | | | - Oleg L. Orlov
- International Complex Research Laboratory for Study of Climate Change, Land Use and BiodiversityUniversity of TyumenTyumenRussia
- Department of BiochemistryUral State Medical UniversityEkaterinburgRussia
| | - Maria V. Orlova
- International Complex Research Laboratory for Study of Climate Change, Land Use and BiodiversityUniversity of TyumenTyumenRussia
- Laboratory of Biodiversity MonitoringNational Research Tomsk State UniversityTomskRussia
| | | | - Matthias Göttsche
- Faunistisch‐ Ökologische Arbeitsgemeinschaft, AG WirbeltiereChristian‐Albrechts‐Universität KielKielGermany
| | | | | | - Morten Elmeros
- Department of BioscienceKalø, Aarhus UniversityGrenåDenmark
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33
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Molecular Phylogenetics of Bradypus (Three-Toed Sloth, Pilosa: Bradypodidae, Mammalia) and Phylogeography of Bradypus variegatus (Brown-Throated Three-Toed Sloth) with Mitochondrial Gene Sequences. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09465-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Rakotoarivelo AR, O'Donoghue P, Bruford MW, Moodley Y. Rapid ecological specialization despite constant population sizes. PeerJ 2019; 7:e6476. [PMID: 31041147 PMCID: PMC6476403 DOI: 10.7717/peerj.6476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/17/2019] [Indexed: 11/20/2022] Open
Abstract
Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik's bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in East Africa, with Scriptus dispersing to colonise suitable habitats west of the African Rift and Sylvaticus radiating from east of the Rift into southern Africa via a series of mainly vicariance events. Discussion Despite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik's bushbuck relative to the phenotypically similar montane bushbuck in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continent's extant large mammalian diversity.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Limpopo, Republic of South Africa.,Natiora Ahy, Antananarivo, Madagascar
| | - Paul O'Donoghue
- Specialist Wildlife Services, Specialist Wildlife Services, St Asaph, United Kingdom
| | - Michael W Bruford
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Limpopo, Republic of South Africa
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Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards. Mol Phylogenet Evol 2019; 134:269-281. [PMID: 30763758 DOI: 10.1016/j.ympev.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 11/20/2022]
Abstract
Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.
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Rakotoarivelo AR, Goodman SM, Schoeman MC, Willows-Munro S. Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 2019; 7:e5866. [PMID: 30671293 PMCID: PMC6339777 DOI: 10.7717/peerj.5866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
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Affiliation(s)
- Andrinajoro R. Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Limpopo, South Africa
- School of Life Sciences, University of Kwa-Zulu Natal, Pietermaritzburg, Kwa-Zulu Natal, South Africa
- Natiora Ahy, Antananarivo, Madagascar
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, IL, United States of America
- Association Vahatra, Antananarivo, Madagascar
| | - M. Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Westville, Kwa-Zulu Natal, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwa-Zulu Natal, Pietermaritzburg, Kwa-Zulu Natal, South Africa
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Barrasso DA, Basso NG. Low genetic divergence but many names in the endemic Patagonian frogs of the genus
Atelognathus
(Anura, Batrachylidae): A molecular genetic and morphological perspective. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diego Andrés Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus‐CONICET) Puerto Madryn Chubut Argentina
- Facultad de Ciencias Naturales y Ciencias de la SaludUniversidad Nacional de la Patagonia “San Juan Bosco” (UNPSJB) Puerto Madryn Chubut Argentina
| | - Néstor Guillermo Basso
- Instituto de Diversidad y Evolución Austral (IDEAus‐CONICET) Puerto Madryn Chubut Argentina
- Facultad de Ciencias Naturales y Ciencias de la SaludUniversidad Nacional de la Patagonia “San Juan Bosco” (UNPSJB) Puerto Madryn Chubut Argentina
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38
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Walton K, Marshall BA, Phillips NE, Verry AJF, Ritchie PA. Phylogeography of the New Zealand whelksCominella maculosaandC. virgata(Gastropoda: Neogastropoda: Buccinoidea: Buccinidae). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Kerry Walton
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Bruce A Marshall
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Nicole E Phillips
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alexander J F Verry
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Peter A Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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How Many Species, Taxa, or Lineages of Cebus albifrons (Platyrrhini, Primates) Inhabit Ecuador? Insights from Mitogenomics. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Robertson DR, Dominguez-Dominguez O, Victor B, Simoes N. An Indo-Pacific damselfish ( Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction. PeerJ 2018; 6:e4328. [PMID: 29441235 PMCID: PMC5807916 DOI: 10.7717/peerj.4328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/15/2018] [Indexed: 11/20/2022] Open
Abstract
The Indo-West Pacific (IWP) coral-reef damselfish Neopomacentrus cyanomos is well established across the south-west Gulf of Mexico (SwGoMx). Comparisons of mtDNA sequences of the SwGoMx population with those from conspecifics from 16 sites scattered across its native geographic range show that the SwGoMx population is derived from two of four native lineages: one from the north-west Pacific Ocean, the other from the northern Indian Ocean. Three hypotheses address how this species was introduced to the SwGoMX: (1) aquarium release; (2) borne by cargo-ship; and (3) carried by offshore petroleum platform (petro-platform). The first is unlikely because this species rarely features in the aquarium trade, and “N. cyanomos” traded to the USA from the sole IWP source we are aware of are a misidentified congener, N. taeniurus. The second hypothesis is unlikely because shipping has not been associated with the introduction of alien damselfishes, there is little international shipping between the IWP and the SwGoMx, and voyages between those areas would be lengthy and along environmentally unfavorable routes. Various lines of evidence support the third hypothesis: (i) bio-fouled petro-platforms represent artificial reefs that can sustain large and diverse populations of tropical reef-fishes, including N. cyanomos in the SwGoMx; (ii) relocation of such platforms has been implicated in trans-oceanic introductions leading to establishment of non-native populations of such fishes; and (iii) genetic characteristics of the SwGoMx population indicate that it was established by a large and diverse group of founders drawn from the IWP regions where many petro-platforms currently in the SwGoMx and other Atlantic offshore oilfields originated.
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Affiliation(s)
- D Ross Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Omar Dominguez-Dominguez
- Laboratorio de Biologia Acuatica, Facultad de Biologia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacan, Mexico.,Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Benjamin Victor
- Guy Harvey Research Institute, Nova Southeastern University, Ft Lauderdale, FL, United States of America
| | - Nuno Simoes
- Unidad Multidisciplinaria en Docencia e Investigacion de Sisal, Facultad de Ciencias, UNAM, Sisal, Yucatan, Mexico.,Laboratorio Nacional de Resiliencia Costera, Unidad Académica de Yucatán, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico.,Harte Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
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41
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Lee SJ, Lee MY, Lin LK, Lin YK, Li Y, Shin EH, Han SH, Min MS, Lee H, Kim KS. Phylogeography of the Asian lesser white-toothed shrew, Crocidura shantungensis, in East Asia: role of the Korean Peninsula as refugium for small mammals. Genetica 2018; 146:211-226. [DOI: 10.1007/s10709-018-0014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
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42
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Yost CL, Jackson LJ, Stone JR, Cohen AS. Subdecadal phytolith and charcoal records from Lake Malawi, East Africa imply minimal effects on human evolution from the ∼74 ka Toba supereruption. J Hum Evol 2018; 116:75-94. [PMID: 29477183 DOI: 10.1016/j.jhevol.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 01/27/2023]
Abstract
The temporal proximity of the ∼74 ka Toba supereruption to a putative 100-50 ka human population bottleneck is the basis for the volcanic winter/weak Garden of Eden hypothesis, which states that the eruption caused a 6-year-long global volcanic winter and reduced the effective population of anatomically modern humans (AMH) to fewer than 10,000 individuals. To test this hypothesis, we sampled two cores collected from Lake Malawi with cryptotephra previously fingerprinted to the Toba supereruption. Phytolith and charcoal samples were continuously collected at ∼3-4 mm (∼8-9 yr) intervals above and below the Toba cryptotephra position, with no stratigraphic breaks. For samples synchronous or proximal to the Toba interval, we found no change in low elevation tree cover, or in cool climate C3 and warm season C4 xerophytic and mesophytic grass abundance that is outside of normal variability. A spike in locally derived charcoal and xerophytic C4 grasses immediately after the Toba eruption indicates reduced precipitation and die-off of at least some afromontane vegetation, but does not signal volcanic winter conditions. A review of Toba tuff petrological and melt inclusion studies suggest a Tambora-like 50 to 100 Mt SO2 atmospheric injection. However, most Toba climate models use SO2 values that are one to two orders of magnitude higher, thereby significantly overestimating the amount of cooling. A review of recent genetic studies finds no support for a genetic bottleneck at or near ∼74 ka. Based on these previous studies and our new paleoenvironmental data, we find no support for the Toba catastrophe hypothesis and conclude that the Toba supereruption did not 1) produce a 6-year-long volcanic winter in eastern Africa, 2) cause a genetic bottleneck among African AMH populations, or 3) bring humanity to the brink of extinction.
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Affiliation(s)
- Chad L Yost
- Department of Geosciences, University of Arizona, 1040 E 4th St., Tucson, AZ 85721, USA.
| | - Lily J Jackson
- Department of Geological Sciences, University of Texas at Austin, 2275 Speedway Stop C9000, Austin, TX 78712, USA
| | - Jeffery R Stone
- Department of Earth and Environmental Systems, Indiana State University, Terre Haute, IN 47809, USA
| | - Andrew S Cohen
- Department of Geosciences, University of Arizona, 1040 E 4th St., Tucson, AZ 85721, USA
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43
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Kindler C, Graciá E, Fritz U. Extra-Mediterranean glacial refuges in barred and common grass snakes (Natrix helvetica, N. natrix). Sci Rep 2018; 8:1821. [PMID: 29379101 PMCID: PMC5788984 DOI: 10.1038/s41598-018-20218-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
Extra-Mediterranean glacial refugia of thermophilic biota, in particular in northern latitudes, are controversial. In the present study we provide genetic evidence for extra-Mediterranean refugia in two species of grass snake. The refuge of a widely distributed western European lineage of the barred grass snake (Natrix helvetica) was most likely located in southern France, outside the classical refuges in the southern European peninsulas. One genetic lineage of the common grass snake (N. natrix), distributed in Scandinavia, Central Europe and the Balkan Peninsula, had two distinct glacial refuges. We show that one was located in the southern Balkan Peninsula. However, Central Europe and Scandinavia were not colonized from there, but from a second refuge in Central Europe. This refuge was located in between the northern ice sheet and the Alpine glaciers of the last glaciation and most likely in a permafrost region. Another co-distributed genetic lineage of N. natrix, now massively hybridizing with the aforementioned lineage, survived the last glaciation in a structured refuge in the southern Balkan Peninsula, according to the idea of 'refugia-within-refugia'. It reached Central Europe only very recently. This study reports for the first time the glacial survival of a thermophilic egg-laying reptile species in Central Europe.
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Affiliation(s)
- Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Eva Graciá
- Ecology Area, Department of Applied Biology, Miguel Hernández University, Av. de la Universidad, Torreblanca, 03202, Elche, Spain
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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44
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Genetic diversity of a hitchhiker and prized food source in the Anthropocene: the Asian green mussel Perna viridis (Mollusca, Mytilidae). Biol Invasions 2018. [DOI: 10.1007/s10530-018-1659-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Blinkhorn J, Petraglia MD. Environments and Cultural Change in the Indian Subcontinent. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/693462] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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46
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Saldarriaga-Córdoba M, Parkinson CL, Daza JM, Wüster W, Sasa M. Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE). PLoS One 2017; 12:e0187969. [PMID: 29176806 PMCID: PMC5703453 DOI: 10.1371/journal.pone.0187969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/30/2017] [Indexed: 11/18/2022] Open
Abstract
The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species’ distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O´Higgins, Santiago, Chile
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Juan M. Daza
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Wolfgang Wüster
- School of Biological Sciences, Bangor University, Bangor, United states of Kingdom
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
- Organization for Tropical Studies, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- * E-mail:
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47
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Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption. Sci Rep 2017; 7:16227. [PMID: 29176629 PMCID: PMC5701162 DOI: 10.1038/s41598-017-16430-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/03/2017] [Indexed: 11/28/2022] Open
Abstract
Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.
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48
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Shirley MH, Austin JD. Did Late Pleistocene climate change result in parallel genetic structure and demographic bottlenecks in sympatric Central African crocodiles, Mecistops and Osteolaemus? Mol Ecol 2017; 26:6463-6477. [PMID: 29024142 DOI: 10.1111/mec.14378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 01/24/2023]
Abstract
The mid-Holocene has had profound demographic impacts on wildlife on the African continent, although there is little known about the impacts on species from Central Africa. Understanding the impacts of climate change on codistributed species can enhance our understanding of ecosystem dynamics and for formulating restoration objectives. We took a multigenome comparative approach to examine the phylogeographic structure of two poorly known Central African crocodile species-Mecistops sp. aff. cataphractus and Osteolaemus tetraspis. In addition, we conducted coalescent-based demographic reconstructions to test the hypothesis that population decline was driven by climate change since the Last Glacial Maximum, vs. more recent anthropogenic pressures. Using a hierarchical Bayesian model to reconstruct demographic history, we show that both species had dramatic declines (>97%) in effective population size in the 'period following the Last Glacial Maximum 1,500-18,000 YBP. Identification of genetic structuring showed both species have similar regional structure corresponding to major geological features (i.e., hydrologic basin) and that small observed differences between them are best explained by the differences in their ecology and the likely impact that climate change had on their habitat needs. Our results support our hypothesis that climatic effects, presumably on forest and wetland habitat, had a congruent negative impact on both species.
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Affiliation(s)
- Matthew H Shirley
- Tropical Conservation Institute, Florida International University, Biscayne Bay Campus, North Miami, FL, USA.,Rare Species Conservatory Foundation, Loxahatchee, FL, USA
| | - James D Austin
- Department of Wildlife Ecology & Conservation, University of Florida, Gainesville, FL, USA
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49
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Trewick SA, Pilkington S, Shepherd LD, Gibb GC, Morgan-Richards M. Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response. Mol Ecol 2017; 26:5752-5772. [PMID: 28805283 DOI: 10.1111/mec.14323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/01/2022]
Abstract
The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island-South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.
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Affiliation(s)
- Steve A Trewick
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Stephen Pilkington
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Lara D Shepherd
- Te Papa Tongarewa Museum of New Zealand, Wellington, New Zealand
| | - Gillian C Gibb
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Mary Morgan-Richards
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
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50
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Sana S, Hardouin EA, Gozlan RE, Ercan D, Tarkan AS, Zhang T, Andreou D. Origin and invasion of the emerging infectious pathogen Sphaerothecum destruens. Emerg Microbes Infect 2017; 6:e76. [PMID: 28831194 PMCID: PMC5583672 DOI: 10.1038/emi.2017.64] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/07/2017] [Accepted: 06/23/2017] [Indexed: 11/19/2022]
Abstract
Non-native species are often linked to the introduction of novel pathogens with detrimental effects on native biodiversity. Since Sphaerothecum destruens was first discovered as a fish pathogen in the United Kingdom, it has been identified as a potential threat to European fish biodiversity. Despite this parasite’s emergence and associated disease risk, there is still a poor understanding of its origin in Europe. Here, we provide the first evidence to support the hypothesis that S. destruens was accidentally introduced to Europe from China along with its reservoir host Pseudorasbora parva via the aquaculture trade. This is the first study to confirm the presence of S. destruens in China, and it has expanded the confirmed range of S. destruens to additional locations in Europe. The demographic analysis of S. destruens and its host P. parva in their native and invasive range further supported the close association of both species. This research has direct significance and management implications for S. destruens in Europe as a non-native parasite.
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Affiliation(s)
- Salma Sana
- Bournemouth University, Faculty of Science and Technology, Fern Barrow, Talbot Campus, Poole, Dorset BH12 5BB, UK
| | - Emilie A Hardouin
- Bournemouth University, Faculty of Science and Technology, Fern Barrow, Talbot Campus, Poole, Dorset BH12 5BB, UK
| | - Rodolphe E Gozlan
- UMR BOREA IRD-MNHN-Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, 47 Rue Cuvier, Paris, Cedex 5 75231, France
| | - Didem Ercan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Kötekli, Muğla 48000, Turkey
| | - Ali Serhan Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Kötekli, Muğla 48000, Turkey
| | - Tiantian Zhang
- Bournemouth University, Faculty of Science and Technology, Fern Barrow, Talbot Campus, Poole, Dorset BH12 5BB, UK
| | - Demetra Andreou
- Bournemouth University, Faculty of Science and Technology, Fern Barrow, Talbot Campus, Poole, Dorset BH12 5BB, UK
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