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Gilbert E, Žagar A, López-Darias M, Megía-Palma R, Lister KA, Jones MD, Carretero MA, Serén N, Beltran-Alvarez P, Valero KCW. Environmental factors influence cross-talk between a heat shock protein and an oxidative stress protein modification in the lizard Gallotia galloti. PLoS One 2024; 19:e0300111. [PMID: 38470891 DOI: 10.1371/journal.pone.0300111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Better understanding how organisms respond to their abiotic environment, especially at the biochemical level, is critical in predicting population trajectories under climate change. In this study, we measured constitutive stress biomarkers and protein post-translational modifications associated with oxidative stress in Gallotia galloti, an insular lizard species inhabiting highly heterogeneous environments on Tenerife. Tenerife is a small volcanic island in a relatively isolated archipelago off the West coast of Africa. We found that expression of GRP94, a molecular chaperone protein, and levels of protein carbonylation, a marker of cellular stress, change across different environments, depending on solar radiation-related variables and topology. Here, we report in a wild animal population, cross-talk between the baseline levels of the heat shock protein-like GRP94 and oxidative damage (protein carbonylation), which are influenced by a range of available temperatures, quantified through modelled operative temperature. This suggests a dynamic trade-off between cellular homeostasis and oxidative damage in lizards adapted to this thermally and topologically heterogeneous environment.
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Affiliation(s)
- Edward Gilbert
- School of Natural Sciences, The University of Hull, Hull, United Kingdom
- Energy and Environment Institute, The University of Hull, Hull, United Kingdom
| | - Anamarija Žagar
- National Institute of Biology, Ljubljana, Slovenia
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Campus de Vairão, Vairão, Portugal
| | - Marta López-Darias
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Rodrigo Megía-Palma
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Campus de Vairão, Vairão, Portugal
- Universidad de Alcalá (UAH), Biomedicine and Biotechnology, Alcalá de Henares, Madrid, Spain
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Karen A Lister
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | - Max Dolton Jones
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, United States of America
| | - Miguel A Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Campus de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nina Serén
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto Campus de Vairão, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Beltran-Alvarez
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | - Katharina C Wollenberg Valero
- School of Natural Sciences, The University of Hull, Hull, United Kingdom
- School of Biology and Environmental Science, University College Dublin, Belfield Campus, Dublin, Ireland
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2
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Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Chaouch M, Maretto F, Cendron F, Charfi-Cheikhrouha F, Ben Abderrazak S, Djemali M, Cassandro M. Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds. Genes (Basel) 2022; 13:genes13081421. [PMID: 36011332 PMCID: PMC9408117 DOI: 10.3390/genes13081421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.
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Affiliation(s)
- Yousra Ben Sassi-Zaidy
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Aziza Mohamed-Brahmi
- Laboratory of Agricultural Production Systems Sustainability in the North Western Region of Tunisia, Department of Animal Production, Ecole Supérieure d’Agriculture du Kef Boulifa, University of Jendouba, Le Kef 7119, Tunisia
| | - Melek Chaouch
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fabio Maretto
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
| | - Filippo Cendron
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Faouzia Charfi-Cheikhrouha
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Souha Ben Abderrazak
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Mnaour Djemali
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
| | - Martino Cassandro
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
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Städele V, Arandjelovic M, Nixon S, Bergl RA, Bradley BJ, Breuer T, Cameron KN, Guschanski K, Head J, Kyungu JC, Masi S, Morgan DB, Reed P, Robbins MM, Sanz C, Smith V, Stokes EJ, Thalmann O, Todd A, Vigilant L. The complex Y-chromosomal history of gorillas. Am J Primatol 2022; 84:e23363. [PMID: 35041228 DOI: 10.1002/ajp.23363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/27/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022]
Abstract
Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.
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Affiliation(s)
- Veronika Städele
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Evolutionary and Anthropocene Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Stuart Nixon
- Field Programmes and Conservation Science, Chester Zoo, North of England Zoological Society, Chester, UK
| | | | - Brenda J Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, USA
| | - Thomas Breuer
- WWF Germany, Berlin, Germany.,Mbeli Bai Study, Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Katerina Guschanski
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.,Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Shelly Masi
- Eco-Anthropologie, Muséum National d'Histoire Naturelle, CNRS, Musée de l'Homme, Université de Paris, Paris, France
| | - David B Morgan
- Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Crickette Sanz
- Department of Anthropology, Washington University in Saint Louis, Saint Louis, Missouri, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Emma J Stokes
- Wildlife Conservation Society, Global Conservation Program, New York City, New York, USA
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Škraba Jurlina D, Marić A, Mrdak D, Kanjuh T, Špelić I, Nikolić V, Piria M, Simonović P. Alternative Life-History in Native Trout (Salmo spp.) Suppresses the Invasive Effect of Alien Trout Strains Introduced Into Streams in the Western Part of the Balkans. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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5
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Bohórquez-Alonso ML, Mesa-Avila G, Suárez-Rancel M, Font E, Molina-Borja M. Predictors of contest outcome in males of two subspecies of Gallotia galloti (Squamata: Lacertidae). Behav Ecol Sociobiol 2018. [DOI: 10.1007/s00265-018-2480-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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7
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Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C, Poncet V, De Kochko A, Rakotomalala JJ, Hamon P. Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. ANNALS OF BOTANY 2013; 111:229-48. [PMID: 23275631 PMCID: PMC3555535 DOI: 10.1093/aob/mcs283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated. METHODS Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species. KEY RESULTS Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity. CONCLUSIONS Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.
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8
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Versieux LM, Barbará T, Wanderley MDGL, Calvente A, Fay MF, Lexer C. Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography. Mol Phylogenet Evol 2012; 64:177-89. [DOI: 10.1016/j.ympev.2012.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 03/04/2012] [Accepted: 03/23/2012] [Indexed: 11/16/2022]
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Yuan J, Cheng F, Zhou S. Genetic structure of the tree peony (Paeonia rockii) and the Qinling Mountains as a geographic barrier driving the fragmentation of a large population. PLoS One 2012; 7:e34955. [PMID: 22523566 PMCID: PMC3327690 DOI: 10.1371/journal.pone.0034955] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/08/2012] [Indexed: 11/23/2022] Open
Abstract
Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars.
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Affiliation(s)
- Jun–hui Yuan
- Landscape Architecture College of Beijing Forestry University, Haidian District, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Haidian District, Beijing, China
- Gansu Forestry Technological College, Tianshui, Gansu, China
| | - Fang–Yun Cheng
- Landscape Architecture College of Beijing Forestry University, Haidian District, Beijing, China
- National Flower Engineering Research Center, Key Laboratory for the Genetic and Breeding of Forestry Trees and Ornamental Plants, Beijing, China
- * E-mail: (SZ); (FC)
| | - Shi–Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Haidian District, Beijing, China
- * E-mail: (SZ); (FC)
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10
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Laurence S, Coltman DW, Gorrell JC, Schulte-Hostedde AI. Genetic structure of muskrat (Ondatra zibethicus) and its concordance with taxonomy in North America. J Hered 2011; 102:688-96. [PMID: 21810770 DOI: 10.1093/jhered/esr071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extrinsic factors such as physical barriers play an important role in shaping population genetic structure. A reduction in gene flow leading to population structuring may ultimately lead to population divergence. These divergent populations are often considered subspecies. Because genetic differentiation may represent differences between subspecies, patterns of genetic structure should reflect subspecies groupings. In this study, we examine the contemporary population genetic structure of muskrat (n = 331) and assess the relevance of 4 geographically distinct subspecies designations across northern North America using 9 microsatellite loci. We predicted that patterns of gene flow and genetic structure would reflect the described subspecies. We found evidence of genetic differentiation between western and eastern regions, and muskrats from Newfoundland (NF) showed significantly lower genetic diversity than central regions. A strong isolation by distance pattern was also detected within the eastern cluster. Our results did not differentiate Ondatra zibethicus spatulus (northwest) from O. z. albus (central), but they suggest a distinction between O. z. obscurus (NF) and O. z. zibethicus (east). This study highlights the need for more phylogenetic studies in order to better understand intraspecific divergence and the genetic characterization of subspecies.
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Affiliation(s)
- Sophie Laurence
- Department of Biology, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario, Canada.
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11
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Nater A, Nietlisbach P, Arora N, van Schaik CP, van Noordwijk MA, Willems EP, Singleton I, Wich SA, Goossens B, Warren KS, Verschoor EJ, Perwitasari-Farajallah D, Pamungkas J, Krützen M. Sex-Biased Dispersal and Volcanic Activities Shaped Phylogeographic Patterns of Extant Orangutans (genus: Pongo). Mol Biol Evol 2011; 28:2275-88. [DOI: 10.1093/molbev/msr042] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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12
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Divergence times and colonization of the Canary Islands by Gallotia lizards. Mol Phylogenet Evol 2010; 56:747-57. [PMID: 20307675 DOI: 10.1016/j.ympev.2010.03.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/10/2010] [Accepted: 03/12/2010] [Indexed: 11/21/2022]
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13
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Gayral P, Blondin L, Guidolin O, Carreel F, Hippolyte I, Perrier X, Iskra-Caruana ML. Evolution of endogenous sequences of banana streak virus: what can we learn from banana (Musa sp.) evolution? J Virol 2010; 84:7346-59. [PMID: 20427523 PMCID: PMC2898222 DOI: 10.1128/jvi.00401-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 04/22/2010] [Indexed: 11/20/2022] Open
Abstract
Endogenous plant pararetroviruses (EPRVs) are viral sequences of the family Caulimoviridae integrated into the nuclear genome of numerous plant species. The ability of some endogenous sequences of Banana streak viruses (eBSVs) in the genome of banana (Musa sp.) to induce infections just like the virus itself was recently demonstrated (P. Gayral et al., J. Virol. 83:6697-6710, 2008). Although eBSVs probably arose from accidental events, infectious eBSVs constitute an extreme case of parasitism, as well as a newly described strategy for vertical virus transmission in plants. We investigated the early evolutionary stages of infectious eBSV for two distinct BSV species-GF (BSGFV) and Imové (BSImV)-through the study of their distribution, insertion polymorphism, and structure evolution among selected banana genotypes representative of the diversity of 60 wild Musa species and genotypes. To do so, the historical frame of host evolution was analyzed by inferring banana phylogeny from two chloroplast regions-matK and trnL-trnF-as well as from the nuclear genome, using 19 microsatellite loci. We demonstrated that both BSV species integrated recently in banana evolution, circa 640,000 years ago. The two infectious eBSVs were subjected to different selective pressures and showed distinct levels of rearrangement within their final structure. In addition, the molecular phylogenies of integrated and nonintegrated BSVs enabled us to establish the phylogenetic origins of eBSGFV and eBSImV.
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Gortat T, Gryczyńska-Siemiątkowska A, Rutkowski R, Kozakiewicz A, Mikoszewski A, Kozakiewicz M. Landscape pattern and genetic structure of a yellow-necked mouse Apodemus flavicollis population in north-eastern Poland. ACTA ACUST UNITED AC 2010. [DOI: 10.4098/j.at.0001-7051.102.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Makowsky R, Cox CL, Roelke C, Chippindale PT. Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses. Mol Phylogenet Evol 2010; 57:485-94. [PMID: 20472081 DOI: 10.1016/j.ympev.2010.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
Abstract
Determining the appropriate gene for phylogeny reconstruction can be a difficult process. Rapidly evolving genes tend to resolve recent relationships, but suffer from alignment issues and increased homoplasy among distantly related species. Conversely, slowly evolving genes generally perform best for deeper relationships, but lack sufficient variation to resolve recent relationships. We determine the relationship between sequence divergence and Bayesian phylogenetic reconstruction ability using both natural and simulated datasets. The natural data are based on 28 well-supported relationships within the subphylum Vertebrata. Sequences of 12 genes were acquired and Bayesian analyses were used to determine phylogenetic support for correct relationships. Simulated datasets were designed to determine whether an optimal range of sequence divergence exists across extreme phylogenetic conditions. Across all genes we found that an optimal range of divergence for resolving the correct relationships does exist, although this level of divergence expectedly depends on the distance metric. Simulated datasets show that an optimal range of sequence divergence exists across diverse topologies and models of evolution. We determine that a simple to measure property of genetic sequences (genetic distance) is related to phylogenic reconstruction ability in Bayesian analyses. This information should be useful for selecting the most informative gene to resolve any relationships, especially those that are difficult to resolve, as well as minimizing both cost and confounding information during project design.
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Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Box 19498, Arlington, TX 76019, USA.
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Gu XD, Liu SY, Wang YZ, Wu H. Development and characterization of eleven polymorphic microsatellite loci from South China field mouse (Apodemus draco). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9868-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Buschiazzo E, Gemmell NJ. Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes. AUST J ZOOL 2009. [DOI: 10.1071/zo09038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.
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Tennessen JA, Blouin MS. Balancing selection at a frog antimicrobial peptide locus: fluctuating immune effector alleles? Mol Biol Evol 2008; 25:2669-80. [PMID: 18799711 PMCID: PMC2582982 DOI: 10.1093/molbev/msn208] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host–pathogen coevolution and the ability of species to resist disease epidemics.
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Hrbek T, Crossa M, Farias IP. Conservation strategies for Arapaima gigas (Schinz, 1822) and the Amazonian várzea ecosystem. BRAZ J BIOL 2007; 67:909-17. [DOI: 10.1590/s1519-69842007000500015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 09/12/2007] [Indexed: 11/22/2022] Open
Abstract
In the present study we report a spatial autocorrelation analysis of molecular data obtained for Arapaima gigas, and the implication of this study for conservation and management. Arapaima is an important, but critically over-exploited giant food fish of the Amazonian várzea. Analysis of 14 variable microsatellite loci and 2,347 bp of mtDNA from 126 individuals sampled in seven localities within the Amazon basin suggests that Arapaima forms a continuous population with extensive genetic exchange among localities. Weak effect of isolation-by-distance is observed in microsatellite data, but not in mtDNA data. Spatial autocorrelation analysis of genetic and geographic data suggests that genetic exchange is significantly restricted at distances greater than 2,500 km. We recommend implementing a source-sink metapopulation management and conservation model by proposing replicate high quality várzea reserves in the upper, central, and lower Amazon basin. This conservation strategy would: 1) preserve all of the current genetic diversity of Arapaima; 2) create a set of reserves to supply immigrants for locally depleted populations; 3) preserve core várzea areas in the Amazon basin on which many other species depend. We stress that conservation strategies should not only preserve current genetic diversity, but also the evolutionary processes which have generated the observed patterns.
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Affiliation(s)
- T. Hrbek
- Universidade Federal do Amazonas, Brazil; University of Puerto Rico, Puerto Rico
| | - M. Crossa
- Instituto de Pesquisa Ambiental da Amazônia, Brazil
| | - IP. Farias
- Universidade Federal do Amazonas, Brazil
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Ochieng JW, Steane DA, Ladiges PY, Baverstock PR, Henry RJ, Shepherd M. Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae). Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000600016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Roy V, Demanche C, Livet A, Harry M. Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers. BMC Evol Biol 2006; 6:102. [PMID: 17123444 PMCID: PMC1687204 DOI: 10.1186/1471-2148-6-102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 11/23/2006] [Indexed: 11/18/2022] Open
Abstract
Background Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies. Results Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve. Conclusion Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters.
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Affiliation(s)
- Virginie Roy
- UMR 137 Biosol, UFR de Sciences, Université Paris XII – Val de Marne, av. du Général de Gaulle, 94010 Créteil cedex, France
| | - Christine Demanche
- UMR 137 Biosol, UFR de Sciences, Université Paris XII – Val de Marne, av. du Général de Gaulle, 94010 Créteil cedex, France
- Faculté de Pharmacie, Laboratoire de Parasitologie, 3 rue du Pr. Laguesse, 59006 Lille, France
| | - Alexandre Livet
- UMR 137 Biosol, UFR de Sciences, Université Paris XII – Val de Marne, av. du Général de Gaulle, 94010 Créteil cedex, France
| | - Myriam Harry
- UMR 137 Biosol, UFR de Sciences, Université Paris XII – Val de Marne, av. du Général de Gaulle, 94010 Créteil cedex, France
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Johnsen A, Andersson S, Fernandez JG, Kempenaers B, Pavel V, Questiau S, Raess M, Rindal E, Lifjeld JT. Molecular and phenotypic divergence in the bluethroat (Luscinia svecica) subspecies complex. Mol Ecol 2006; 15:4033-47. [PMID: 17054501 DOI: 10.1111/j.1365-294x.2006.03075.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subspecies complexes may provide valuable insights into the early stages of the speciation process. The bluethroat (Luscinia svecica) consists of many morphologically distinct subspecies that differ most strikingly in the ornamental colour pattern of the male throat. We investigated the genetic and phenotypic differentiation in this subspecies complex, using (i) microsatellite genotyping (11 loci) of a sample of 364 individuals from bluethroat populations in Europe and Asia, and (ii) spectrometric and morphological measurements of a sample of 131 museum skin specimens. Population genetic analyses, based on microsatellite allele frequency variation, revealed a slight but significant overall population differentiation (F(ST) = 0.042). There was a well-differentiated southern group of subspecies with white or no throat spots and a less-differentiated northern group of chestnut-spotted populations. Phylogenetic analyses indicated that the southern all-blue and white-spotted forms are ancestral to the chestnut-spotted subspecies. In addition to the qualitative variation in throat plumage pattern already described in the literature, we found significant quantitative variation among subspecies in hue, chroma and brightness of the ultraviolet (UV)/blue throat coloration, and this variation seemed to be unrelated to the phylogenetic distance between subspecies.
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Affiliation(s)
- Arild Johnsen
- National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, 0318 Oslo, Norway
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Ciofi C, Wilson GA, Beheregaray LB, Marquez C, Gibbs JP, Tapia W, Snell HL, Caccone A, Powell JR. Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island. Genetics 2006; 172:1727-44. [PMID: 16387883 PMCID: PMC1456292 DOI: 10.1534/genetics.105.047860] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Accepted: 12/13/2005] [Indexed: 11/18/2022] Open
Abstract
Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.
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Affiliation(s)
- Claudio Ciofi
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
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Grassi F, Labra M, Minuto L, Casazza G, Sala F. Natural hybridization in Saxifraga callosa Sm. PLANT BIOLOGY (STUTTGART, GERMANY) 2006; 8:243-52. [PMID: 16547869 DOI: 10.1055/s-2005-873047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Saxifraga callosa Sm. is an evergreen perennial species distributed from Eastern Spain, through the Western Alps and the Apennines, to southern Italy. The existence of high morphological variation within different subspecies indicates that phenotypic characters are useful but not sufficient taxonomic tools. Indeed, available morphological data already suggested that S. callosa subentity lantoscana may be an outcross between S. callosa and S. cochlearis. In this work, by analyzing ITS (Internal Transcribed Sequences), AFLP (Amplified Fragment Length Polymorphisms), and cpDNA (chloroplast DNA) markers, a comprehensive study of the genomic relationships among S. callosa and related species has been carried out. The sequence of the ITS region of S. callosa subentity lantoscana gave no conclusive results on the taxonomy status of S. callosa subentity lantoscana. On the other hand, the use of the "NewHybrids" software to analyze an AFLP data-set (208 polymorphic amplified fragments) supported a significant posterior probability that S. callosa subentity lantoscana individuals are natural hybrids between S. callosa and S. cochlearis. The level of introgression of genes from alien genomes was confirmed by a simpler and quick methodology that analyze length variation in cpDNA sequences.
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Affiliation(s)
- F Grassi
- Botanical Garden, Department of Biology, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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Hughes M, Möller M, Bellstedt DU, Edwards TJ, de Villiers M. Refugia, dispersal and divergence in a forest archipelago: a study of Streptocarpus in eastern South Africa. Mol Ecol 2005; 14:4415-26. [PMID: 16313602 DOI: 10.1111/j.1365-294x.2005.02756.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We describe a scenario of plant speciation across a relict forest archipelago in South Africa involving Pleistocene habitat expansion-contraction cycles, dispersal and adaptation to lower temperatures. This is the first population level study using molecular data in South African forests and has significant implications for conservation efforts in this area. Populations of the mesophytic forest floor herbs Streptocarpus primulifolius sensu lato and Streptocarpus rexii were sampled throughout their range in the naturally fragmented forests of eastern South Africa in order to investigate population genetic and phylogenetic patterns within the species complex, using nuclear microsatellites, nuclear ribosomal ITS (internal transcribed spacer) sequences and chloroplast genome sequences. S. primulifolius harbours high levels of genetic diversity at both the nuclear (mean HE = 0.50) and the chloroplast level (each population fixed for a unique haplotype). This is consistent with populations of these coastal species being Pleistocene relicts. In contrast, populations of S. rexii in cooler habitats at higher altitudes and lower latitudes harbour little or no nuclear genetic diversity (mean HE = 0.09) and most share a common chloroplast haplotype. The split of S. rexii from populations intermediate between the two species (S. cf. primulifolius) occurred between 0 and 0.44 million years ago according to the calibrated ITS phylogeny of the taxa. The low genetic diversity and homogeneity of S. rexii is congruent with this species having reached its current range during the Holocene. We found no evidence of monophyly of any of the taxa in this study, which we consider a consequence of recent evolution in a fragmented habitat.
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Affiliation(s)
- M Hughes
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK.
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26
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BLOOR PAUL, BROWN RICHARDP. Morphological variation in Gallotia atlantica from the volcanic island of Lanzarote: subspecies designations and recent lava flows. Biol J Linn Soc Lond 2005. [DOI: 10.1111/j.1095-8312.2005.00496.x] [Citation(s) in RCA: 4] [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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27
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Stenson AG, Thorpe RS, Malhotra A. Evolutionary differentiation of bimaculatus group anoles based on analyses of mtDNA and microsatellite data. Mol Phylogenet Evol 2005; 32:1-10. [PMID: 15186792 DOI: 10.1016/j.ympev.2003.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2001] [Revised: 11/25/2003] [Indexed: 11/20/2022]
Abstract
The bimaculatus group of anoles inhabit the northern Lesser Antilles, as far south as Dominica. This study uses 1005 base pairs (bp) of mitochondrial DNA sequence data from two genes, cytochrome b (521 bp) and cytochrome oxidase subunit I (484 bp) to reconstruct phylogenetic relationships between species and populations of anoles from all islands banks. Allele frequency data from nuclear microsatellite loci are also analysed to assess their utility in uncovering historical relationships and provide independent corroboration for the mtDNA tree. Although the number of microsatellite loci used (six) was relatively small, some essential elements of the mitochondrial DNA phylogeny were recovered successfully. Anoles from Terre de Haut, Les Saintes, previously described as a subspecies of Anolis marmoratus, are shown to be more closely related to A. oculatus and their elevation to a full species, A. terraealtae, is supported. An island colonisation sequence inferred from the phylogeny shows a general pattern of North-to South colonisation. However, the Saban anole, A. sabanus, is shown to be derived from A. marmoratus populations from western Basse Terre following a longer-range, south to north translocation.
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Affiliation(s)
- Andrew G Stenson
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, UK.
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28
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Ajzenberg D, Bañuls AL, Su C, Dumètre A, Demar M, Carme B, Dardé ML. Genetic diversity, clonality and sexuality in Toxoplasma gondii. Int J Parasitol 2004; 34:1185-96. [PMID: 15380690 DOI: 10.1016/j.ijpara.2004.06.007] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Revised: 06/28/2004] [Accepted: 06/28/2004] [Indexed: 11/15/2022]
Abstract
The majority of Toxoplasma gondii strains from a variety of human and animal sources have been grouped into three highly clonal but closely related lineages. The low occurrence of nucleotide differences among the three predominant lineages and their unusual dimorphic allelic composition suggest that they have arisen from a recent common ancestry. Less than 1% of the previously studied strains contain unique genotypes and high divergence of DNA sequence, and therefore are considered 'exotic' or 'atypical' strains. The seemingly low genetic diversity in T. gondii may have been underestimated because most parasite strains in previous studies were collected from human patients and domestic animals in North America and Europe. To investigate the genetic diversity of T. gondii, we analysed parasite strains isolated from remote geographical regions by multilocus microsatellite sequencing and phylogenetic analysis. The genetic diversity indices, the molecular analysis of microsatellite genotypes and the constructed phylogram considered together suggest that the global T. gondii population is highly diversified and not characteristic of a clonal organism. The most parsimonious hypothesis is that T. gondii presents a complex population structure with a mix of clonal and sexual propagation as a function of the environmental conditions. The comparison between domestic strains data on one hand and wild strains data on the other hand is in favour of more frequent sexual recombinations in wild environment even though Toxoplasma subpopulation in human and domestic animals is largely clonal.
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Affiliation(s)
- D Ajzenberg
- Laboratoire de Parasitologie-Mycologie, EA3174, Faculté de Médecine, 2 rue du Dr Marcland, 87031 Limoges, France
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29
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GLAUBRECHT MATTHIAS, KÖHLER FRANK. Radiating in a river: systematics, molecular genetics and morphological differentiation of viviparous freshwater gastropods endemic to the Kaek River, central Thailand (Cerithioidea, Pachychilidae). Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00361.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Allan GJ, Francisco-Ortega J, Santos-Guerra A, Boerner E, Zimmer EA. Molecular phylogenetic evidence for the geographic origin and classification of Canary Island Lotus (Fabaceae: Loteae). Mol Phylogenet Evol 2004; 32:123-38. [PMID: 15186802 DOI: 10.1016/j.ympev.2003.11.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2003] [Revised: 11/12/2003] [Indexed: 11/18/2022]
Abstract
Molecular phylogenetic analyses of Macaronesian Lotus and related genera were conducted to assess their biogeographic history and taxonomy. Macaronesian Lotus, which are typically classified within one of two subgenera, Lotus subgenus Pedrosia or L. subg. Rhyncholotus, are diagnosed by the presence of a forked or toothed style and differences in corolla morphology. Maximum parsimony and Bayesian analyses of internal transcribed spacer sequences identify a well-supported northwest African-Cape Verde Island clade that includes all members of Lotus subgenus Pedrosia+L. subg. Rhyncholotus. There is modest support for two independently nested clades containing the Canary Island species and two non-Canarian species, Lotus assakensis from Africa and Lotus azoricus endemic to the Azores. Biogeographic reconstruction based on a parsimony topology unequivocally identifies an African origin for the Canary Island group with subsequent back dispersal to the African continent and a single dispersal event to the Azores. A phylogeographic assessment of colonization and diversification patterns suggests that geographic isolation via interisland colonization of ecologically similar habitats is the primary mode of species diversification in Canary Island Lotus.
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Affiliation(s)
- G J Allan
- Department of Biological Sciences, Northern Arizona University, South Beaver Street, Bldg 21, Flagstaff, AZ 86011, USA.
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31
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Arévalo E, Zhu Y, Carpenter JM, Strassmann JE. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters. BMC Evol Biol 2004; 4:8. [PMID: 15070433 PMCID: PMC385225 DOI: 10.1186/1471-2148-4-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 03/02/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera) using 69 species. RESULTS Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. CONCLUSION The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.
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Affiliation(s)
- Elisabeth Arévalo
- Department of Biology, Providence College, Providence, RI, 02918-0001, USA
| | - Yong Zhu
- Department of Epidemiology and Public Health, Yale University, 60 College Street, P.O. Box 208034, New Haven, CT 06520-8034, USA
| | - James M Carpenter
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024-5192, USA
| | - Joan E Strassmann
- Department of Ecology and Evolutionary Biology, MS 170, Rice University, 6100 Main St., Houston, TX 77005-1892, USA
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Novick RR, Dick CW, Lemes MR, Navarro C, Caccone A, Bermingham E. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis. Mol Ecol 2004; 12:2885-93. [PMID: 14629370 DOI: 10.1046/j.1365-294x.2003.01951.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation.
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Affiliation(s)
- Rachel Roth Novick
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA.
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Chung SM, Decker-Walters DS, Staub JE. Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses. ACTA ACUST UNITED AC 2003. [DOI: 10.1139/b03-074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate genetic relationships in Benincaseae (19 accessions), Cucurbiteae (1), Joliffieae (2), Melothrieae (2), and Sicyeae (3) tribes of the family Cucurbitaceae, consensus chloroplast simple sequence repeats (ccSSR) primer pairs obtained from tobacco (Nicotiana tabacum L.) chloroplast DNA were used. Variation in the length and putative sequence substitution events of polymerase chain reaction (PCR) products were analyzed. Sequencing of four fragments (ccSSR-1, -7, -8, and -19) revealed that convergence in fragment length occurs in more distant species comparisons. In ccSSR-1 and -8, the same fragment lengths occurred as the result of different insertion and deletion events. Nevertheless, the examination of a large number of ccSSR fragments suggested that this apparent homoplasy could be overshadowed by evolutionary relationships among taxa. This hypothesis is supported by the relative degree of positive congruence of taxon groupings after cluster and principal components analyses performed on both base pair length and sequence substitution data. Moreover, these analyses support previous biochemical and morphological data indicating that distinct lineages exist within the Benincaseae. Likewise, data support the hypotheses that the genus Benincasa is descended from an ancient African ancestor and that the progenitor of the New World Sicyeae tribe shares a common ancestor with the genus Luffa of the Old World Benincaseae.Key words: Benincaseae, chloroplast, consensus, homoplasy, microsatellite, simple sequence repeats.
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Abstract
Genetic variability among populations of orangutans from Borneo and Sumatra was assessed using seven SSR loci. Most SSR loci were highly polymorphic and their allele frequencies exhibited substantial variation across subpopulations. While significant genetic subdivision was observed among the island populations, genetic distance did not increase with geographic distance and sufficient gene flow persists to prevent marked genetic subdivision. Since it is unlikely that the Bornean Orangutans dispersed naturally among locations separated by such formidable geographic barriers, human assistance might already have altered their genetic structure. Our data suggests that there may be at least two subspecific clades of orangutans within Borneo while Central Kalimantan animals may have become more genetically related to animals in Sumatra due to human intervention.
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Affiliation(s)
- Sreetharan Kanthaswamy
- Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, Iowa 52246, USA.
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Koskinen MT, Nilsson J, Veselov AJ, Potutkin AG, Ranta E, Primmer CR. Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae. Heredity (Edinb) 2002; 88:391-401. [PMID: 11986877 DOI: 10.1038/sj.hdy.6800072] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2001] [Accepted: 01/15/2002] [Indexed: 11/08/2022] Open
Abstract
The phylogeography of an endangered salmonid, European grayling (Thymallus thymallus), was studied based on analysis of 17 nuclear microsatellite DNA loci. In agreement with earlier mitochondrial DNA (mtDNA) studies, phylogenetic relationships of the populations suggested that northern Europe was colonized from two distinct Pleistocene refugia. Furthermore, microsatellites revealed highly supported grouping of mainland Swedish, Norwegian, Danish, German and Slovenian populations, suggesting that grayling from the northwestern and central Europe have descended from their southern conspecifics. The level of divergence between populations was substantial, even across short geographical distances. Although this was in part due to postglacial colonization patterns and contemporary barriers for gene flow, the high divergence estimates between hydrologically connected sampling locations implied efficient interpopulation reproductive isolation. Microsatellites revealed that the populations exhibited, on average, only 3.5 (+/-2.2) alleles per locus, indicating that T. thymallus has strikingly low levels of intrapopulation genetic diversity as compared with other freshwater fish species. Accordingly, as indicated by analysis of molecular variance (AMOVA), only 49.1-58.0% of the total grayling microsatellite diversity resided within populations. A latitudinal genetic diversity gradient, potentially resulting from glaciation-mediated founder events, was not evident. Alternatively, it is possible that grayling display limited dispersal behaviour/capability, leading to low long-term effective population sizes and, consequently, depauperate intrapopulation polymorphism. These findings have implications for conservation of T. thymallus. Importantly, they exemplify that microsatellites can be highly informative for intraspecific phylogeography studies dealing with substantial divergence scales.
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Affiliation(s)
- M T Koskinen
- Integrative Ecology Unit, Department of Ecology and Systematics, PO Box 17, 00014 University of Helsinki, Helsinki, Finland.
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