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Kelava S, Mans BJ, Shao R, Moustafa MAM, Matsuno K, Takano A, Kawabata H, Sato K, Fujita H, Ze C, Plantard O, Hornok S, Gao S, Barker D, Barker SC, Nakao R. Phylogenies from mitochondrial genomes of 120 species of ticks: Insights into the evolution of the families of ticks and of the genus Amblyomma. Ticks Tick Borne Dis 2020; 12:101577. [PMID: 33120251 DOI: 10.1016/j.ttbdis.2020.101577] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022]
Abstract
The evolution and phylogenetic relationships of the ticks at both the family and genus levels are contested. The genus Amblyomma and its subgenera are in a state of flux; moreover, the relationships among the three tick families are controversial due to conflicting phylogenetic support for different arrangements of the three families of living ticks. With 18 newly sequenced mitochondrial (mt) genomes of ticks included, we executed the largest mt genome phylogenetic study of ticks so far. Phylogenetic trees were inferred from one sea spider mt genome, one horseshoe crab, five mite mt genomes and 146 tick mt genomes from 120 species: 153 mt genomes in total. Sixteen phylogenetic trees were inferred from 10 datasets using both maximum likelihood and Bayesian inference methods. We describe the first novel mt gene-arrangement for the metastriate Ixodidae in Amblyomma (Africaniella) transversale. Also, three unusual partial 16S rRNA gene inserts were found in the mt genome of Haemaphysalis (Alloceraea) kitaokai: we consider the possible role of past genome translocation events in the formation of these inserts. Our phylogenies revealed evidence that: (i) the genus Amblyomma is polyphyletic with respect to Amblyomma (Africaniella) transversale; (ii) the subgenus Aponomma is apparently embedded in the genus Amblyomma; (iii) Haemaphysalis (Segalia) parva and Haemaphysalis (Alloceraea) kitaokai form a clade to the exclusion of other Haemaphysalis species; and (iv) the phylogenetic position of the family Nuttalliellidae is unstable among phylogenies from different datasets.
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Affiliation(s)
- Samuel Kelava
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Onderstepoort, 0110, South Africa; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0110, South Africa; The Department of Life and Consumer Sciences, University of South Africa, Florida, 1709, South Africa
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4558, Australia
| | | | - Keita Matsuno
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Ai Takano
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiroki Kawabata
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kozue Sato
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, 56-3 Aratano, Anan-shi, Tokushima, 779-1510, Japan
| | - Chen Ze
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | | | - Sandor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, PR China
| | - Dayana Barker
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Ryo Nakao
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
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Zhang D, Li K, Gao J, Liu Y, Gao LZ. The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Catarino D, Knutsen H, Veríssimo A, Olsen EM, Jorde PE, Menezes G, Sannæs H, Stanković D, Company JB, Neat F, Danovaro R, Dell'Anno A, Rochowski B, Stefanni S. The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis). Mol Ecol 2015; 24:6061-79. [PMID: 26547144 DOI: 10.1111/mec.13453] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
Knowledge of the mechanisms limiting connectivity and gene flow in deep-sea ecosystems is scarce, especially for deep-sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and near threatened deep-sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497-bp fragment from the mtDNA control region. High levels of genetic homogeneity across the Atlantic (Φ(ST) = -0.0091, F(ST) = 0.0024, P > 0.05) were found suggesting one large population unit at this basin. The low levels of genetic divergence between Atlantic and Australia (Φ(ST) = 0.0744, P < 0.01; F(ST) = 0.0015, P > 0.05) further suggested that this species may be able to maintain some degree of genetic connectivity even across ocean basins. In contrast, sharks from the Mediterranean Sea exhibited marked genetic differentiation from all other localities studied (Φ(ST) = 0.3808, F(ST) = 0.1149, P < 0.001). This finding suggests that the shallow depth of the Strait of Gibraltar acts as a barrier to dispersal and that isolation and genetic drift may have had an important role shaping the Mediterranean shark population over time. Analyses of life history traits allowed the direct comparison among regions providing a complete characterization of this shark's populations. Sharks from the Mediterranean had markedly smaller adult body size and size at maturity compared to Atlantic and Pacific individuals. Together, these results suggest the existence of an isolated and unique population of C. coelolepis inhabiting the Mediterranean that most likely became separated from the Atlantic in the late Pleistocene.
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Affiliation(s)
- Diana Catarino
- MARE-Marine and Environmental Sciences Centre, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal
| | - Halvor Knutsen
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway.,University of Agder, Kristiansand, N-4604, Norway.,Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Ana Veríssimo
- CIBIO-U.P., Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, 4485-661, Portugal.,College of William and Mary, Virginia Institute of Marine Science, Route 1208, Greate Road, Gloucester Point, 23062, VA, USA
| | - Esben Moland Olsen
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway.,University of Agder, Kristiansand, N-4604, Norway.,Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Per Erik Jorde
- Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Gui Menezes
- MARE-Marine and Environmental Sciences Centre, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal
| | - Hanne Sannæs
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway
| | - David Stanković
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, Trieste, 34127, Italy
| | - Joan Baptista Company
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Spain
| | - Francis Neat
- Marine Laboratory, Marine Scotland-Science, PO Box 101, 375 Victoria Road, Aberdeen, AB11 9DB, UK
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, 60131, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, 60131, Italy
| | - Bastien Rochowski
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Sergio Stefanni
- IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,CNR-ISSIA, Via de Marini 6, Genova, 16149, Italy
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Royston SR, Carr SM. Conservation genetics of high-arctic Gull species at risk: I. Diversity in the mtDNA control region of circumpolar populations of the Endangered Ivory Gull (Pagophila eburnea). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3995-3999. [PMID: 25541301 DOI: 10.3109/19401736.2014.989520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The high-arctic Ivory Gull (Pagophila eburnea) has recently undergone a sharp decline in numbers, and in Canada it is listed as "Endangered" under the Species-At-Risk Act. To test for circumpolar genetic distinctiveness, we examined 264 bp of the mtDNA Control Region Domain I from 127 museum specimens collected during the breeding season from northern Canada, Greenland, and Norway, and during the non-breeding season from adjacent overwintering grounds in Canada, Greenland, and a disjunct area in Alaska adjacent to the Bering Sea. Partition of genetic variance according to various phylogeographic and breeding ground models indicates no strong population structure, except that Alaska birds are consistently differentiated from other locations, and there are significant temporal shifts in haplotype frequencies. The evidence suggests that Ivory Gulls in Canada, Greenland, and Norway are a single genetic entity, in contrast to Alaska birds, which may represent a distinctive Siberian population.
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Affiliation(s)
- Stephanie R Royston
- a Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland , St John's , NL , Canada
| | - Steven M Carr
- a Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland , St John's , NL , Canada
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A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0343-0] [Citation(s) in RCA: 3] [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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Andrews KR, Perrin WF, Oremus M, Karczmarski L, Bowen BW, Puritz JB, Toonen RJ. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers. Mol Ecol 2013; 22:2408-23. [DOI: 10.1111/mec.12193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/26/2022]
Affiliation(s)
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Marc Oremus
- Opération Cétacés; 16 rue Henri Niautou 98800 Nouméa New Caledonia
| | - Leszek Karczmarski
- The Swire Institute of Marine Science; School of Biological Sciences; The University of Hong Kong; Cape d'Aguilar Shek O Hong Kong
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
| | | | - Robert J. Toonen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
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Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A. Identification of species by multiplex analysis of variable-length sequences. Nucleic Acids Res 2010; 38:e203. [PMID: 20923781 PMCID: PMC3001097 DOI: 10.1093/nar/gkq865] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing.
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Affiliation(s)
- Filipe Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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Dawe KL, Shafer ABA, Herman TB, Stewart DT. Diffusion of nuclear and mitochondrial genes across a zone of secondary contact in the maritime shrew, Sorex maritimensis: implications for the conservation of a Canadian endemic mammal. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9645-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Egan AN, Crandall KA. Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae). Mol Phylogenet Evol 2007; 46:532-46. [PMID: 18039582 DOI: 10.1016/j.ympev.2007.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 09/27/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
The impact of including insertion/deletion events as phylogenetic characters was explored within North American Psoraleeae (Leguminosae). This comprehensive analysis of the impact of gap character incorporation spanned four different indel coding schemes, gaps coded as missing characters, simple binary characters, multi-state characters, and as a 5th state, across two optimality criteria: maximum parsimony and Bayesian Inference. Two nuclear (ITS and Waxy) and six chloroplast (trnS/G, trnL/F, trnK, matK, trnD/T, and rpoB-trnC) DNA regions were sequenced from 43 species of North American Psoraleeae as the foundation of the study. Our results suggest that gaps can provide a substantial percentage of informative characters and can increase phylogenetic resolution and nodal branch support. Phylogenetic signal within indels was higher in chloroplast regions relative to nuclear regions, demonstrating their inclusion as especially important in chloroplast-based phylogenetic studies. Phylogenetic analysis of generic relationships within Psoraleeae is largely congruent with that proposed by Grimes (1990) with a few exceptions. New World species are supported as a monophyletic group. Our analyses suggest that Otholobium may need to be split into two genera and that Psoralidium is polyphyletic and will require movement of Psoralidium tenuiflorum to Pediomelum.
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Affiliation(s)
- Ashley N Egan
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
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Gómez-Díaz E, González-Solis J. Geographic assignment of seabirds to their origin: combining morphologic, genetic, and biogeochemical analyses. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2007; 17:1484-98. [PMID: 17708223 DOI: 10.1890/06-1232.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Longline fisheries, oil spills, and offshore wind farms are some of the major threats increasing seabird mortality at sea, but the impact of these threats on specific populations has been difficult to determine so far. We tested the use of molecular markers, morphometric measures, and stable isotope (delta15N and delta13C) and trace element concentrations in the first primary feather (grown at the end of the breeding period) to assign the geographic origin of Calonectris shearwaters. Overall, we sampled birds from three taxa: 13 Mediterranean Cory's Shearwater (Calonectris diomedea diomedea) breeding sites, 10 Atlantic Cory's Shearwater (Calonectris diomedea borealis) breeding sites, and one Cape Verde Shearwater (C. edwardsii) breeding site. Assignment rates were investigated at three spatial scales: breeding colony, breeding archipelago, and taxa levels. Genetic analyses based on the mitochondrial control region (198 birds from 21 breeding colonies) correctly assigned 100% of birds to the three main taxa but failed in detecting geographic structuring at lower scales. Discriminant analyses based on trace elements composition achieved the best rate of correct assignment to colony (77.5%). Body measurements or stable isotopes mainly succeeded in assigning individuals among taxa (87.9% and 89.9%, respectively) but failed at the colony level (27.1% and 38.0%, respectively). Combining all three approaches (morphometrics, isotopes, and trace elements on 186 birds from 15 breeding colonies) substantially improved correct classifications (86.0%, 90.7%, and 100% among colonies, archipelagos, and taxa, respectively). Validations using two independent data sets and jackknife cross-validation confirmed the robustness of the combined approach in the colony assignment (62.5%, 58.8%, and 69.8% for each validation test, respectively). A preliminary application of the discriminant model based on stable isotope delta15N and delta13C values and trace elements (219 birds from 17 breeding sites) showed that 41 Cory's Shearwaters caught by western Mediterranean long-liners came mainly from breeding colonies in Menorca (48.8%), Ibiza (14.6%), and Crete (31.7%). Our findings show that combining analyses of trace elements and stable isotopes on feathers can achieve high rates of correct geographic assignment of birds in the marine environment, opening new prospects for the study of seabird mortality at sea.
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Affiliation(s)
- Elena Gómez-Díaz
- Department Biologia Animal (Vertebrats), Av. Diagonal 645, Barcelona 08028, Spain.
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Calibration of a molecular clock in tits (Paridae)—Do nucleotide substitution rates of mitochondrial genes deviate from the 2% rule? Mol Phylogenet Evol 2007; 44:1-14. [DOI: 10.1016/j.ympev.2007.03.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 12/18/2006] [Accepted: 03/05/2007] [Indexed: 11/18/2022]
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12
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Stewart FJ, Cavanaugh CM. Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J Mol Evol 2007; 65:44-67. [PMID: 17568983 DOI: 10.1007/s00239-006-0235-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Variation in the internal transcribed spacer (ITS) of the rRNA (rrn) operon is increasingly used to infer population-level diversity in bacterial communities. However, intragenomic ITS variation may skew diversity estimates that do not correct for multiple rrn operons within a genome. This study characterizes variation in ITS length, tRNA composition, and intragenomic nucleotide divergence across 155 Bacteria genomes. On average, these genomes encode 4.8 rrn operons (range: 2-15) and contain 2.4 unique ITS length variants (range: 1-12) and 2.8 unique sequence variants (range: 1-12). ITS variation stems primarily from differences in tRNA gene composition, with ITS regions containing tRNA-Ala + tRNA-Ile (48% of sequences), tRNA-Ala or tRNA-Ile (10%), tRNA-Glu (11%), other tRNAs (3%), or no tRNA genes (27%). Intragenomic divergence among paralogous ITS sequences grouped by tRNA composition ranges from 0% to 12.11% (mean: 0.94%). Low divergence values indicate extensive homogenization among ITS copies. In 78% of alignments, divergence is <1%, with 54% showing zero variation and 81% containing at least two identical sequences. ITS homogenization occurs over relatively long sequence tracts, frequently spanning the entire ITS, and is largely independent of the distance (basepairs) between operons. This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family.
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Affiliation(s)
- Frank J Stewart
- Department of Organismic and Evolutionary Biology, Harvard University, The Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Davison A, Chiba S. The recent history and population structure of five Mandarina snail species from subtropical Ogasawara (Bonin Islands, Japan). Mol Ecol 2006; 15:2905-19. [PMID: 16911210 DOI: 10.1111/j.1365-294x.2006.02990.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of Pleistocene climate change on the organisms of tropical and subtropical regions is rather poorly understood. We therefore studied the land snail genus Mandarina (Bradybaenidae) of oceanic Ogasawara (Bonin Islands, Japan), with the aim of using population genetic data to understand their recent history. Our analysis of a mitochondrial 16S ribosomal RNA region from more than 600 snails in five ground-living species suggests that populations on the small islands of Mukoujima, Anejima, Imotojima and Meijima, as well as on the low-lying southern and central parts of Hahajima, have probably undergone recent bottlenecks followed by subsequent expansions. Except between the main island of Hahajima and Mukouijima, there is almost no evidence for gene flow among islands even though the islands were connected repeatedly by land bridges through the Pleistocene. Within islands the population structure is severe, suggestive of a long-term, low level of gene flow (F(ST) is frequently greater than 0.5 among geographically close populations). Finally, there is a marked genetic patchiness, meaning that genetically close populations are sometimes separated by genetically distant populations. These patterns could be a consequence of expansion from bottlenecks, low active dispersal and founder effects caused by rare long-distance migrants. Unfortunately, the exact nature of the refugia and bottlenecks remains unknown because the palaeoclimate of this region is poorly understood. Dating the population size changes is also challenging because the molecular clock is uncertain. We suggest, however, that arid conditions or deforestation induced by decreased atmospheric CO(2) may have been the main factor in determining population size.
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Affiliation(s)
- Angus Davison
- Institute of Genetics, School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
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