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Fukutani K, Matsui M, Tran DV, Nishikawa K. Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate. PeerJ 2022; 10:e13452. [PMID: 35698618 PMCID: PMC9188313 DOI: 10.7717/peerj.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads (Bufo japonicus and B. torrenticola) and the demography of each lineage from the past to the present based on mitochondrial sequences and ecological niche models. Japanese toads are a monophyletic group with two main clades (clades A and B). Clade A represents B. j. formosus, including three clades (clades A1, A2, and A3). Clade B contains three clades, two of which corresponded to B. j. japonicus (clades B1 and B2) and the other to B. torrenticola. Clade B2 and B. torrenticola made a sister group, and, thus, B. j. japonicus is paraphyletic. Clades A and B diverged in the late Miocene 5.7 million years ago (Mya) during the period when the Japanese archipelago was constructed. The earliest divergence between the three clades of clade A was estimated at 1.8 Mya. Clades A1 and A2 may have diverged at 0.8 Mya, resulting from the isolation in the multiple different refugia; however, the effects of the glacial climate on the divergence events of clade A3 are unclear. Divergences within clade B occurred from the late Pliocene to the early Pleistocene (3.2-2.2 Mya). Niche similarity between the parapatric clade in clade B (clades B1 and B2) indicated their allopatric divergence. It was suggested that niche segregation between B. japonicus and B. torrenticola contributed to a rapid adaptation of B. torrenticola for lotic breeding. All clade of Japanese toads retreated to each refugium at a low elevation in the glacial period, and effective population sizes increased to construct the current populations after the Last Glacial Maximum. Furthermore, we highlight the areas of climate stability from the last glacial maximum to the present that have served as the refugia of Japanese toads and, thus, affected their present distribution patterns.
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Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Dung Van Tran
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan,Wildlife Department, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan,Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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2
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Mmonwa KL, Barker NP, McQuaid CD, Teske PR. Coastal dunefields maintain pre-Holocene genetic structure in a rocky shore red alga. JOURNAL OF PHYCOLOGY 2021; 57:1542-1553. [PMID: 33982309 DOI: 10.1111/jpy.13182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Most intertidal algae have limited dispersal potential, and areas that lack hard substratum suitable for attachment are thus expected to isolate regional populations from each other. Here, we used nuclear and mitochondrial genetic data to compare genetic structure in two co-distributed intertidal red algae with different dispersal potential along the South African coastline. Gelidium pristoides is divided into a south-eastern and a south-western evolutionary lineage separated by extensive, continuous sandy shoreline habitat adjacent to coastal dunefields. In contrast, Hypnea spicifera is genetically homogeneous throughout its range. In G. pristoides, the genetic breaks are associated with contemporary coastal dunefields. The age of the divergence event suggests that this may reflect the effect of older dispersal barriers, and that genetic structure was subsequently maintained by the formation of contemporary coastal dunefields.
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Affiliation(s)
- Kolobe Lucas Mmonwa
- Research and Monitoring, KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
| | - Nigel Paul Barker
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - Christopher David McQuaid
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Peter Rodja Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
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Levicoy D, Flores K, Rosenfeld S, Cárdenas L. Phylogeography and genetic diversity of the microbivalve Kidderia subquadrata, reveals new data from West Antarctic Peninsula. Sci Rep 2021; 11:5705. [PMID: 33707560 PMCID: PMC7952419 DOI: 10.1038/s41598-021-85042-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
It is well established that Antarctic biodiversity has been strongly influenced by rapid climatic fluctuations during the Quaternary. Marine invertebrates from Antarctica constitute an interesting lens through which to study the impacts of the last glacial periods as glaciation impacted the distribution and intraspecific genetic variation of these animals. However, the impact on the spatial genetic distribution and historical demography of local processes in areas adjacent to the West Antarctic Peninsula (WAP) is less clear. Here we present new genetic information on the bivalve Kidderia subquadrata, a small mollusk that inhabits intertidal rocky island ecosystems throughout the WAP. Using a phylogeographical approach, we examined the spatial patterns of genetic diversity in this brooder species to test the hypothesis of strong genetic structure in incubating organisms and the hypothesis of glacial refugia in organisms with limited dispersion. We found evidence of strong genetic structure among populations of the WAP and a recent expansion in the South Shetland Islands. Our findings are concordant with the predictions that incubating organisms, abundant in Antarctica, present a strong genetic structure among their populations and also support the hypothesis of glacial refugia in organisms with limited dispersion. The effect of the coastal current pattern in the WAP is suggested as a driver to the local spatial dynamics of the genetic diversity distribution. Although genetic information about this microbivalve is still scarce, the knowledge reported here has increased our understanding of the evolutionary patterns of this organism that is endemic to the Southern Ocean.
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Affiliation(s)
- Daniela Levicoy
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile
| | - Kamilla Flores
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecosistemas Marinos Antárticos Y Subantárticos, Universidad de Magallanes, Casilla 113-D, Punta Arenas, Chile.,Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile.,Instituto de Ecología y Biodiversidad (IEB), Las Palmeras # 3425, Ñuñoa, Santiago, Chile
| | - Leyla Cárdenas
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile.
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4
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Hart MW, Puritz JB. Correction to ‘Extraordinarily rapid life-history divergence between
Cryptasterina
sea star species'. Proc Biol Sci 2020; 287:20201325. [DOI: 10.1098/rspb.2020.1325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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5
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McKeown NJ, Gwilliam MP, Healey AJE, Skujina I, Potts WM, Sauer WHH, Shaw PW. Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma. JOURNAL OF FISH BIOLOGY 2020; 96:1434-1443. [PMID: 32154919 DOI: 10.1111/jfb.14316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/27/2019] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.
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Affiliation(s)
- Niall J McKeown
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael P Gwilliam
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Amy J E Healey
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ilze Skujina
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Warren M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Warwick H H Sauer
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Paul W Shaw
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
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Healey AJE, Farthing MW, Nunoo FKE, Potts WM, Sauer WHH, Skujina I, King N, de Becquevort S, Shaw PW, McKeown NJ. Genetic analysis provides insights into species distribution and population structure in East Atlantic horse mackerel (Trachurus trachurus and T. capensis). JOURNAL OF FISH BIOLOGY 2020; 96:795-805. [PMID: 32031244 PMCID: PMC7079130 DOI: 10.1111/jfb.14276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
Two sister species of horse mackerel (Trachurus trachurus and T. capensis) are described that are intensively harvested in East Atlantic waters. To address long-standing uncertainties as to their respective geographical ranges, overlap and intraspecific population structure this study combined genetic (mitochondrial DNA and microsatellite) analysis and targeted sampling of the hitherto understudied West African coast. mtDNA revealed two reciprocally monophyletic clades corresponding to each species with interspecies nuclear differentiation supported by FST values. The T. trachurus clade was found across the north-east Atlantic down to Ghana but was absent from Angolan and South African samples. The T. capensis clade was found only in South Africa, Angola and a single Ghanaian individual. This pattern suggests that both species may overlap in the waters around Ghana. The potential for cryptic hybridization and/or indiscriminate harvesting of both species in the region is discussed. For T. capensis mtDNA supports high gene flow across the Benguela upwelling system, which fits with the species' ecology. The data add to evidence of a lack of significant genetic structure throughout the range of T. trachurus though the assumption of demographic panmixia is cautioned against. For both species, resolution of stock recruitment heterogeneity relevant to fishery management, as well as potential hybridization, will require more powerful genomic analyses.
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Affiliation(s)
- Amy J. E. Healey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Matthew W. Farthing
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | | | - Warren M. Potts
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Warwick H. H. Sauer
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Ilze Skujina
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nathan King
- School of Ocean SciencesBangor UniversityMenai Bridge, AngleseyUK
| | - Sophie de Becquevort
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Paul W. Shaw
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Niall J. McKeown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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Korábek O, Juřičková L, Petrusek A. Inferring the sources of postglacial range expansion in two large European land snails. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ondřej Korábek
- Department of Ecology Faculty of Science Charles University Praha Czechia
| | - Lucie Juřičková
- Department of Zoology Faculty of Science Charles University Praha Czechia
| | - Adam Petrusek
- Department of Ecology Faculty of Science Charles University Praha Czechia
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Solecki AM, Skevington JH, Buddle CM, Wheeler TA. Phylogeography of higher Diptera in glacial and postglacial grasslands in western North America. BMC Ecol 2019; 19:53. [PMID: 31861996 PMCID: PMC6923875 DOI: 10.1186/s12898-019-0266-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times. RESULTS Two geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium. CONCLUSIONS Populations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.
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Affiliation(s)
- Anna M. Solecki
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1 Canada
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
| | - Jeffrey H. Skevington
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids, and Nematodes, 960 Carling Ave, Ottawa, ON K1A 0C6 Canada
| | - Christopher M. Buddle
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
| | - Terry A. Wheeler
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
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9
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Sakuma K, Ishida R, Kodama T, Takada Y. Reconstructing the population history of the sandy beach amphipod Haustorioides japonicus using the calibration of demographic transition (CDT) approach. PLoS One 2019; 14:e0223624. [PMID: 31596891 PMCID: PMC6785125 DOI: 10.1371/journal.pone.0223624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/24/2019] [Indexed: 11/19/2022] Open
Abstract
Calibration of the molecular rate is one of the major challenges in marine population genetics. Although the use of an appropriate evolutionary rate is crucial in exploring population histories, calibration of the rate is always difficult because fossil records and geological events are rarely applicable for rate calibration. The acceleration of the evolutionary rate for recent coalescent events (or more simply, the time dependency of the molecular clock) is also a problem that can lead to overestimation of population parameters. Calibration of demographic transition (CDT) is a rate calibration technique that assumes a post-glacial demographic expansion, representing one of the most promising approaches for dealing with these potential problems in the rate calibration. Here, we demonstrate the importance of using an appropriate evolutionary rate, and the power of CDT, by using populations of the sandy beach amphipod Haustorioides japonicus along the Japanese coast of the northwestern Pacific Ocean. Analysis of mitochondrial sequences found that the most peripheral population in the Pacific coast of northeastern Honshu Island (Tohoku region) is genetically distinct from the other northwestern Pacific populations. By using the two-epoch demographic model and rate of temperature change, the evolutionary rate was modeled as a log-normal distribution with a median rate of 2.2%/My. The split-time of the Tohoku population was subsequently estimated to be during the previous interglacial period by using the rate distribution, which enables us to infer potential causes of the divergence between local populations along the continuous Pacific coast of Japan.
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Affiliation(s)
- Kay Sakuma
- Japan Sea National Fisheries Research Institute, Fisheries Research and Education Agency, Niigata, Japan
- * E-mail:
| | - Risa Ishida
- Japan Sea National Fisheries Research Institute, Fisheries Research and Education Agency, Niigata, Japan
| | - Taketoshi Kodama
- Japan Sea National Fisheries Research Institute, Fisheries Research and Education Agency, Niigata, Japan
| | - Yoshitake Takada
- Japan Sea National Fisheries Research Institute, Fisheries Research and Education Agency, Niigata, Japan
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Hanazaki K, Tomozawa M, Suzuki Y, Kinoshita G, Yamamoto M, Irino T, Suzuki H. Estimation of Evolutionary Rates of Mitochondrial DNA in Two Japanese Wood Mouse Species Based on Calibrations with Quaternary Environmental Changes. Zoolog Sci 2019; 34:201-210. [PMID: 28589839 DOI: 10.2108/zs160169] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evolutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence patterns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitutions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from analyses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion parameter tau values: 3.9, 5.6-5.7, and 7.8-8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.
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Affiliation(s)
- Kaori Hanazaki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | | | - Yutaro Suzuki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Gohta Kinoshita
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masanobu Yamamoto
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Tomohisa Irino
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species. Heredity (Edinb) 2018; 122:441-457. [PMID: 30171190 DOI: 10.1038/s41437-018-0135-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/27/2018] [Accepted: 06/27/2018] [Indexed: 11/08/2022] Open
Abstract
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an approximate Bayesian computation (ABC) framework to test which scenario best fit the observed genetic data. Simulations indicated that phylogeographic and multilocus population-level sampling both could differentiate among refugial scenarios, although inferences made using mitochondrial data were less accurate when a longer coalescence time was assumed. Furthermore, all empirical genetic datasets were most consistent with expansion from a single refugium based on ABC. Our results indicate a stronger role for post-glacial range expansion, rather than isolation in allopatric refugia followed by range expansion, in structuring diversity in this species. To distinguish among complex historical scenarios, we recommend explicitly modeling the effects of range expansion and evaluating alternate refugial scenarios for wide-ranging taxa.
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Díaz A, Gérard K, González-Wevar C, Maturana C, Féral JP, David B, Saucède T, Poulin E. Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation. PLoS One 2018; 13:e0197611. [PMID: 29874287 PMCID: PMC5991379 DOI: 10.1371/journal.pone.0197611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/04/2018] [Indexed: 01/10/2023] Open
Abstract
One of the most relevant characteristics of the extant Southern Ocean fauna is its resiliency to survive glacial processes of the Quaternary. These climatic events produced catastrophic habitat reductions and forced some marine benthic species to move, adapt or go extinct. The marine benthic species inhabiting the Antarctic upper continental shelf faced the Quaternary glaciations with different strategies that drastically modified population sizes and thus affected the amount and distribution of intraspecific genetic variation. Here we present new genetic information for the most conspicuous regular sea urchin of the Antarctic continental shelf, Sterechinus neumayeri. We studied the patterns of genetic diversity and structure in this broadcast-spawner across three Antarctic regions: Antarctic Peninsula, the Weddell Sea and Adélie Land in East Antarctica. Genetic analyses based on mitochondrial and nuclear markers suggested that S. neumayeri is a single genetic unit around the Antarctic continent. The species is characterized by low levels of genetic diversity and exhibits a typical star-like haplotype genealogy that supports the hypothesis of a single in situ refugium. Based on two mutation rates standardized for this genus, the Bayesian Skyline plot analyses detected a rapid demographic expansion after the Last Glacial Maximum. We propose a scenario of rapid postglacial expansion and recolonization of Antarctic shallow areas from a less ice-impacted refugium where the species survived the LGM. Considering the patterns of genetic diversity and structure recorded in the species, this refugium was probably located in East Antarctica.
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Affiliation(s)
- Angie Díaz
- Departamento de Zoología, Universida d de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Karin Gérard
- Facultad de Ciencias, Universidad de Magallanes, Bulnes, Punta Arenas, Chile
- Laboratorio de Ecología Molecular Antártica y Subantártica, Universidad de Magallanes, Punta Arenas, Chile
| | - Claudio González-Wevar
- Laboratorio de Ecología Molecular Antártica y Subantártica, Universidad de Magallanes, Punta Arenas, Chile
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
| | - Claudia Maturana
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
| | - Jean-Pierre Féral
- UMR 7263—IMBE, Station Marine d’Endoume, Institut Méditerranéen de Biodiversité et d’Ecologie Marine et continentale, Chemin de la Batterie des Lions,Marseille, France
| | - Bruno David
- Biogéosciences, UMR CNRS 6282, Université de Bourgogne, boulevard Gabriel, Dijon, France
- Museum National d’Histoire Naturelle, Paris, France
| | - Thomas Saucède
- UMR 7263—IMBE, Station Marine d’Endoume, Institut Méditerranéen de Biodiversité et d’Ecologie Marine et continentale, Chemin de la Batterie des Lions,Marseille, France
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
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Kitada S, Nakajima K, Hamasaki K. Population panmixia and demographic expansion of a highly piscivorous marine fish Scomberomorus niphonius. JOURNAL OF FISH BIOLOGY 2017; 91:1435-1448. [PMID: 28990668 DOI: 10.1111/jfb.13466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/17/2017] [Indexed: 06/07/2023]
Abstract
Population structure and demographic history of the Japanese Spanish mackerel Scomberomorus niphonius a highly piscivorous and migratory marine fish, were assessed using mitochondrial DNA control region sequences (n = 720) and microsatellite genotypes at five loci (n = 1331) for samples collected on Japanese coasts from 2001 to 2010. The population structure was panmictic and the haplotype and allele frequencies were temporally stable even during the recent recovery process. Demographic expansion was strongly supported throughout the Pleistocene, suggesting that the oscillating glacial and interglacial climate conditions in the Pleistocene had no substantial impact on the demographic history of S. niphonius.
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Affiliation(s)
- S Kitada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - K Nakajima
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - K Hamasaki
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
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Wang ZD, Liao J, Huang CQ, Long SS, Zhang S, Guo YS, Liu L, Liu CW. Significant genetic differentiation of Gobiopterus lacustris, a newly recorded transparent goby in China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:785-791. [PMID: 28752775 DOI: 10.1080/24701394.2017.1357712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.
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Affiliation(s)
- Zhong-Duo Wang
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Jian Liao
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Cheng-Qin Huang
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Shui-Sheng Long
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Shun Zhang
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Yu-Song Guo
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Li Liu
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
| | - Chu-Wu Liu
- a Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College , Guangdong Ocean University , Zhanjiang , China
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Marzouk Z, Aurelle D, Said K, Chenuil A. Cryptic lineages and high population genetic structure in the exploited marine snail Hexaplex trunculus (Gastropoda: Muricidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Eberle J, Rödder D, Beckett M, Ahrens D. Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers. GLOBAL CHANGE BIOLOGY 2017; 23:1988-2004. [PMID: 28063178 DOI: 10.1111/gcb.13616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/22/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
Today, indigenous forests cover less than 0.6% of South Africa's land surface and are highly fragmented. Most forest relicts are very small and typically occur in fire-protected gorges along the eastern Great Escarpment. Yet, they hold a unique and valuable fauna with high endemism and ancient phylogenetic lineages, fostered by long-term climatic stability and complex microclimates. Despite numerous studies on southern African vegetation cover, the current state of knowledge about the natural extension of indigenous forests is rather fragmentary. We use an integrated approach of population-level phylogeography and climatic niche modeling of forest-associated chafer species to assess connectivity and extent of forest habitats since the last glacial maximum. Current and past species distribution models ascertained potential fluctuations of forest distribution and supported a much wider potential current extension of forests based on climatic data. Considerable genetic admixture of mitochondrial and nuclear DNA among many populations and an increase in mean population mutation rate in Extended Bayesian Skyline Plots of all species indicated more extended or better connected forests in the recent past (<5 kya). Genetic isolation of certain populations, as revealed by population differentiation statistics (GST'), as well as landscape connectivity statistics and habitat succession scenarios suggests considerable loss of habitat connectivity. As major anthropogenic influence is likely, conservational actions need to be considered.
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Affiliation(s)
- Jonas Eberle
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Dennis Rödder
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Marc Beckett
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
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Reid K, Hoareau TB, Graves JE, Potts WM, Dos Santos SMR, Klopper AW, Bloomer P. Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb) 2016; 117:307-315. [PMID: 27436525 DOI: 10.1038/hdy.2016.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022] Open
Abstract
The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (FST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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Affiliation(s)
- K Reid
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - T B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - J E Graves
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Williamsburg, VA, USA
| | - W M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - S M R Dos Santos
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - A W Klopper
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - P Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
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