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Sacks BN, Statham MJ, Serieys LEK, Riley SPD. Population Genetics of California Gray Foxes Clarify Origins of the Island Fox. Genes (Basel) 2022; 13:genes13101859. [PMID: 36292742 PMCID: PMC9602142 DOI: 10.3390/genes13101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and in the southern Channel Islands <6000 years ago. It is unclear whether island foxes evolved directly from mainland gray foxes transported to the islands one or more times or from a now-extinct mainland population, already diverged from the gray fox. Our 345 mitochondrial sequences, combined with previous data, confirmed island foxes to be monophyletic, tracing to a most recent common ancestor approximately 85,000 years ago. Our rooted nuclear DNA tree additionally indicated genome-wide monophyly of island foxes relative to western gray foxes, although we detected admixture in northern island foxes from adjacent mainland gray foxes, consistent with some historical gene flow. Southern California gray foxes also bore a genetic signature of admixture and connectivity to a desert population, consistent with partial replacement by a late-Holocene range expansion. Using our outgroup analysis to root previous nuclear sequence-based trees indicated reciprocal monophyly of northern versus southern island foxes. Results were most consistent with island fox origins through multiple introductions from a now-extirpated mainland population.
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Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
- Correspondence:
| | - Mark J. Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
| | | | - Seth P. D. Riley
- National Park Service, Santa Monica Mountains National Recreation Area, 401 W Hillcrest Dr, Thousand Oaks, CA 91360, USA
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Braun de Torrez EC, Frock CF, Boone WW, Sovie AR, McCleery RA. Seasick: Why Value Ecosystems Severely Threatened by Sea-Level Rise? Estuaries Coast 2020; 44:899-910. [PMID: 33100935 PMCID: PMC7568938 DOI: 10.1007/s12237-020-00850-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Climate change will alter natural areas on a global scale within the next century. In areas vulnerable to climate change, scientists are regularly challenged to justify the resources needed for research and conservation. We face what may seem like a losing battle, especially in low-lying coastal areas where sea-level rise is predicted to severely degrade or destroy many ecosystems. Using sea-level rise in the low-elevation state of Florida, USA, as a case study, we argue that it is critical to remain engaged in the research, restoration, and conservation of natural areas threatened by climate change for as long as possible. These areas will continue to provide invaluable ecological and societal benefits. Additionally, uncertainty surrounding climate change forecasts and their ecological impact leaves room for optimism, research, and actions that are necessary for developing adaptation plans and mitigating further sea-level rise and other consequences of climate change. We urge scientists and particularly students beginning their careers not to forego research and conservation efforts of these imperiled lands but to face this unprecedented challenge with determination, creativity, and solution-based strategies.
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Affiliation(s)
- Elizabeth C. Braun de Torrez
- Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, P.O. Box 110430, Gainesville, FL 32611-0430 USA
| | - Catherine F. Frock
- Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, P.O. Box 110430, Gainesville, FL 32611-0430 USA
| | - Wesley W. Boone
- Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, P.O. Box 110430, Gainesville, FL 32611-0430 USA
| | - Adia R. Sovie
- Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, P.O. Box 110430, Gainesville, FL 32611-0430 USA
- Department of Forestry and Natural Resources, University of Kentucky, College of Agriculture Food and the Environment, Thomas Poe Cooper Building, 730 Rose St., Lexington, KY 40546 USA
| | - Robert A. McCleery
- Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, P.O. Box 110430, Gainesville, FL 32611-0430 USA
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Rossi NA, Menchaca-Rodriguez A, Antelo R, Wilson B, McLaren K, Mazzotti F, Crespo R, Wasilewski J, Alda F, Doadrio I, Barros TR, Hekkala E, Alonso-Tabet M, Alonso-Giménez Y, Lopez M, Espinosa-Lopez G, Burgess J, Thorbjarnarson JB, Ginsberg JR, Vliet KA, Amato G. High levels of population genetic differentiation in the American crocodile (Crocodylus acutus). PLoS One 2020; 15:e0235288. [PMID: 32614920 PMCID: PMC7332040 DOI: 10.1371/journal.pone.0235288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus.
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Affiliation(s)
- Natalia A. Rossi
- Wildlife Conservation Society, Bronx, New York, United States of America
- Sackler Institute of Comparative Genomics, American Museum of Natural History, Manhattan, New York, United States of America
- Department of Ecology, Evolution and Environmental Biology, Columbia University, Columbia, New York, United States of America
| | | | - Rafael Antelo
- Fundación Palmarito Casanare, Bogotá, Colombia
- Estación Biológica El Frío, Apure, Venezuela
| | - Byron Wilson
- Department of Life Sciences, University of the West Indies, Mona, Jamaica
| | - Kurt McLaren
- Department of Life Sciences, University of the West Indies, Mona, Jamaica
| | - Frank Mazzotti
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Rafael Crespo
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Joe Wasilewski
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, Florida, United States of America
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Tito R. Barros
- Museo de Biología de la Universidad del Zulia, Maracaibo, Venezuela
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, Bronx, New York, United States of America
| | | | | | - Manuel Lopez
- Refugio de Fauna Monte Cabaniguán-Ojo de Agua, Las Tunas, Cuba
| | | | - Joe Burgess
- US Forest Service, Idleyld Park, Oregon, United States of America
| | | | - Joshua R. Ginsberg
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Kent A. Vliet
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - George Amato
- Sackler Institute of Comparative Genomics, American Museum of Natural History, Manhattan, New York, United States of America
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Abstract
AbstractSince the establishment of the Rare Breeds Survival Trust (RBST) in 1973, rare breed genetic conservation has only gradually emerged as a major key to the continued success and survival of populations. Thus, although basic population and demographic data have been recorded for all breeds listed by the Trust and most rare breeds have kept detailed pedigrees, there is still little information available about current population genetic structure and dynamics over time. Consequently, the majority of rare breed population meta-analyses based upon pedigree data are yet to be carried out. Transfer of rare breed records onto a computer database is therefore a current priority for the RBST, in addition to making available software to provide rare breed organisations with breed profiles to describe founder effects, effective population size (Ne), rate of inbreeding (ΔF), and kinship patterns. Results from rare breed pedigree analyses using this software can now be used to a) illustrate where and how loss of genetic diversity has taken place in rare breeds and b) enable decision processes concerning conservation strategy in future. Conservation strategy informed by such analyses can only be successfully implemented if due regard is given to the realities imposed by the need to maintain rare breed populations within an agricultural context, however. In light of these recent improvements to data recording and access to studies of population genetic structure, some of the traditional limitations to advances to rare breed conservation strategy may now need to be re-examined.
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Singh A, Sharma V, Dikshit HK, Aski M, Kumar H, Thirunavukkarasu N, Patil BS, Kumar S, Sarker A. Association mapping unveils favorable alleles for grain iron and zinc concentrations in lentil (Lens culinaris subsp. culinaris). PLoS One 2017; 12:e0188296. [PMID: 29161321 PMCID: PMC5697819 DOI: 10.1371/journal.pone.0188296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/04/2017] [Indexed: 11/18/2022] Open
Abstract
Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation. The genetic variation among genotypes of the association mapping (AM) panel was characterized using a genetic distance-based and a general model-based clustering method. The model-based analysis identified six subpopulations, which satisfactorily explained the genetic structure of the AM panel. AM analysis identified three SSRs (PBALC 13, PBALC 206, and GLLC 563) associated with grain Fe concentration explaining 9% to 11% of phenotypic variation and four SSRs (PBALC 353, SSR 317-1, PLC 62, and PBALC 217) were associated with grain Zn concentration explaining 14%, to 21% of phenotypic variation. These identified SSRs exhibited consistent performance across locations. These candidate SSRs can be used in marker-assisted genetic improvement for developing Fe and Zn fortified lentil varieties. Favorable alleles and promising genotypes identified in this study can be utilized for lentil biofortification.
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Affiliation(s)
- Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan, India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harish Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Punjab Agriculture University, RRS, Faridkot, Punjab, India
| | | | | | - Shiv Kumar
- ICARDA, B.P. 6299, Station Experiment, INRA-Quich, Rue Hafiane Cherkaoui Agdal, Rabat-Institutes, Rabat, Morocco
| | - Ashutosh Sarker
- South Asia and China Program (ICARDA), NASC Complex, New Delhi, India
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Wallace LE, Wheeler GL, McGlaughlin ME, Bresowar G, Helenurm K. Phylogeography and genetic structure of endemic Acmispon argophyllus and A. dendroideus (Fabaceae) across the California Channel Islands. Am J Bot 2017; 104:743-756. [PMID: 28526725 DOI: 10.3732/ajb.1600429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. METHODS DNA sequences were collected from nuclear (ADH) and plastid genomes (rpL16, ndhA, psbD-trnT) from >450 samples on the Channel Islands and California. We estimated population genetic diversity and structure, phylogenetic patterns among populations, and migration rates, and tested for population growth. KEY RESULTS Populations of northern island A. argophyllus var. niveus are genetically distinct from conspecific populations on southern islands. On the southern islands, A. argophyllus var. argenteus populations on Santa Catalina are phylogenetically distinct from populations of var. argenteus and var. adsurgens on the other southern islands. For A. dendroideus, we found the varieties to be monophyletic. Populations of A. dendroideus var. traskiae on San Clemente are genetically differentiated from other conspecific populations, whereas populations on the northern islands and Santa Catalina show varying degrees of gene flow. Evidence of population growth was found in both species. CONCLUSIONS Oceanic barriers between islands have had a strong influence on population genetic structure in both Acmispon species, although the species have differing phylogeographic patterns. This study provides a contrasting pattern of dispersal on a near island system that does not follow a strict stepping-stone model, commonly found on isolated island systems.
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Affiliation(s)
- Lisa E Wallace
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Gregory L Wheeler
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mitchell E McGlaughlin
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Gerald Bresowar
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Kaius Helenurm
- Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA
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8
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Langin KM, Sillett TS, Funk WC, Morrison SA, Ghalambor CK. Partial support for the central-marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird. Heredity (Edinb) 2017; 119:8-15. [PMID: 28327578 DOI: 10.1038/hdy.2017.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/30/2016] [Accepted: 01/22/2017] [Indexed: 11/09/2022] Open
Abstract
Large-scale population comparisons have contributed to our understanding of the evolution of geographic range limits and species boundaries, as well as the conservation value of populations at range margins. The central-marginal hypothesis (CMH) predicts a decline in genetic diversity and an increase in genetic differentiation toward the periphery of species' ranges due to spatial variation in genetic drift and gene flow. Empirical studies on a diverse array of taxa have demonstrated support for the CMH. However, nearly all such studies come from widely distributed species, and have not considered if the same processes can be scaled down to single populations. Here, we test the CMH on a species composed of a single population: the Island Scrub-Jay (Aphelocoma insularis), endemic to a 250 km2 island. We examined microsatellite data from a quarter of the total population and found that homozygosity increased toward the island's periphery. However, peripheral portions of the island did not exhibit higher genetic differentiation. Simulations revealed that highly localized dispersal and small total population size, but not spatial variation in population density, were critical for generating fine-scale variation in homozygosity. Collectively, these results demonstrate that microevolutionary processes driving spatial variation in genetic diversity among populations can also be important for generating spatial variation in genetic diversity within populations.
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Affiliation(s)
- K M Langin
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - T S Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - W C Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | | | - C K Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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Kronenberger JA, Funk WC, Smith JW, Fitzpatrick SW, Angeloni LM, Broder ED, Ruell EW. Testing the demographic effects of divergent immigrants on small populations of Trinidadian guppies. Anim Conserv 2016. [DOI: 10.1111/acv.12286] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- J. A. Kronenberger
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - W. C. Funk
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - J. W. Smith
- Department of Biology Colorado State University Fort Collins CO USA
| | | | - L. M. Angeloni
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - E. D. Broder
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - E. W. Ruell
- Department of Biology Colorado State University Fort Collins CO USA
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FUNK WCHRIS, LOVICH ROBERTE, HOHENLOHE PAULA, HOFMAN COURTNEYA, MORRISON SCOTTA, SILLETT TSCOTT, GHALAMBOR CAMERONK, MALDONADO JESUSE, RICK TORBENC, DAY MITCHD, POLATO NICHOLASR, FITZPATRICK SARAHW, COONAN TIMOTHYJ, CROOKS KEVINR, DILLON ADAM, GARCELON DAVIDK, KING JULIEL, BOSER CHRISTINAL, GOULD NICHOLAS, ANDELT WILLIAMF. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol 2016; 25:2176-94. [PMID: 26992010 PMCID: PMC4877267 DOI: 10.1111/mec.13605] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 01/02/2023]
Abstract
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
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Affiliation(s)
- W. CHRIS FUNK
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - ROBERT E. LOVICH
- Naval Facilities Engineering Command Southwest, 1220 Pacific Highway, San Diego, CA 92132, USA
| | - PAUL A. HOHENLOHE
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - COURTNEY A. HOFMAN
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | | | - T. SCOTT SILLETT
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013-7012, USA
| | - CAMERON K. GHALAMBOR
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - JESUS E. MALDONADO
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - TORBEN C. RICK
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - MITCH D. DAY
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - NICHOLAS R. POLATO
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - SARAH W. FITZPATRICK
- Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - TIMOTHY J. COONAN
- National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001, USA
| | - KEVIN R. CROOKS
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - ADAM DILLON
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
| | - DAVID K. GARCELON
- Institute for Wildlife Studies, P.O. Box 1104, Arcata, CA 95518, USA
| | - JULIE L. KING
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | | | - NICHOLAS GOULD
- Fisheries, Wildlife, and Conservation Biology, North Carolina State University, Turner House, Box 7646, Raleigh, NC 27695-7646, USA
| | - WILLIAM F. ANDELT
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA
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Robinson JA, Ortega-Del Vecchyo D, Fan Z, Kim BY, vonHoldt BM, Marsden CD, Lohmueller KE, Wayne RK. Genomic Flatlining in the Endangered Island Fox. Curr Biol 2016; 26:1183-9. [PMID: 27112291 DOI: 10.1016/j.cub.2016.02.062] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/11/2022]
Abstract
Genetic studies of rare and endangered species often focus on defining and preserving genetically distinct populations, especially those having unique adaptations [1, 2]. Much less attention is directed at understanding the landscape of deleterious variation, an insidious consequence of geographic isolation and the inefficiency of natural selection to eliminate harmful variants in small populations [3-5]. With population sizes of many vertebrates decreasing and isolation increasing through habitat fragmentation and loss, understanding the extent and nature of deleterious variation in small populations is essential for predicting and enhancing population persistence. The Channel Island fox (Urocyon littoralis) is a dwarfed species that inhabits six of California's Channel Islands and is derived from the mainland gray fox (U. cinereoargenteus). These isolated island populations have persisted for thousands of years at extremely small population sizes [6, 7] and, consequently, are a model for testing ideas about the accumulation of deleterious variation in small populations under natural conditions. Analysis of complete genome sequence data from island foxes shows a dramatic decrease in genome-wide variation and a sharp increase in the homozygosity of deleterious variants. The San Nicolas Island population has a near absence of variation, demonstrating a unique genetic flatlining that is punctuated by heterozygosity hotspots, enriched for olfactory receptor genes and other genes with high levels of ancestral variation. These findings question the generality of the small-population paradigm that maintains substantial genetic variation is necessary for short- and long-term persistence.
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Affiliation(s)
- Jacqueline A Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diego Ortega-Del Vecchyo
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Bernard Y Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Clare D Marsden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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12
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Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 2016; 59:295-310. [PMID: 27064176 DOI: 10.1139/gen-2015-0124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.
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Affiliation(s)
- Richard H Adams
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Heath Blackmon
- b Department of Ecology, Evolution & Behavior, 1987 Upper Buford Cir., University of Minnesota, Saint Paul, MN 55108-6097, USA
| | - Jacobo Reyes-Velasco
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Drew R Schield
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Daren C Card
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Audra L Andrew
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Nyimah Waynewood
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Todd A Castoe
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
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Vanormelingen P, Evans KM, Mann DG, Lance S, Debeer AE, D'Hondt S, Verstraete T, De Meester L, Vyverman W. Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites. Mol Ecol 2015; 24:4433-48. [DOI: 10.1111/mec.13336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Katharine M. Evans
- School of Geosciences; University of Edinburgh; Edinburgh EH9 3JW UK
- Royal Botanic Garden; Edinburgh EH3 5LR UK
| | - David G. Mann
- Royal Botanic Garden; Edinburgh EH3 5LR UK
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); Crta de Poble Nou Km 5.5 E-43540 Sant Carles de la Ràpita Catalunya Spain
| | - Stacey Lance
- Savannah River Ecology Laboratory; University of Georgia; Aiken SC USA
| | - Ann-Eline Debeer
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Sofie D'Hondt
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Tine Verstraete
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; Katholieke Universiteit Leuven; Ch. De Bériotstraat 32 Leuven 3000 Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
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Vartia S, Collins PC, Cross TF, Fitzgerald RD, Gauthier DT, McGinnity P, Mirimin L, Carlsson J. Multiplexing with three-primer PCR for rapid and economical microsatellite validation. Hereditas 2015; 151:43-54. [PMID: 25041267 DOI: 10.1111/hrd2.00044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/20/2014] [Indexed: 02/01/2023] Open
Abstract
The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs were tested, resulting in 73 polymorphic markers. Of these, 55 loci were combined in six multiplex panels each containing between six and eleven markers. Variability of the loci was assessed on G. morhua from the Celtic Sea (n = 46) and the Scotian Shelf (n = 46), two locations that have shown genetic differentiation in previous studies. Multilocus F(ST) between the two samples was estimated at 0.067 (P = 0.001). After three loci potentially under selection were excluded, the global F(ST) was estimated at 0.043 (P = 0.001). Our technique combines three-primer and multiplex PCR techniques, allowing simultaneous screening and validation of relatively large numbers of microsatellite loci.
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Affiliation(s)
- Salla Vartia
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Co. Galway, Ireland; Area 52 Research Group, School of Biology & Environment Science, University College Dublin, Belfield, Dublin, Ireland.
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15
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Hofman CA, Rick TC, Hawkins MTR, Funk WC, Ralls K, Boser CL, Collins PW, Coonan T, King JL, Morrison SA, Newsome SD, Sillett TS, Fleischer RC, Maldonado JE. Mitochondrial genomes suggest rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis). PLoS One 2015; 10:e0118240. [PMID: 25714775 PMCID: PMC4340941 DOI: 10.1371/journal.pone.0118240] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/10/2015] [Indexed: 01/11/2023] Open
Abstract
Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), endemic to California's Channel Islands, and mainland gray foxes (U. cinereoargenteus). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200-7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics.
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Affiliation(s)
- Courtney A. Hofman
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
- * E-mail:
| | - Torben C. Rick
- Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Melissa T. R. Hawkins
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Katherine Ralls
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Christina L. Boser
- The Nature Conservancy, San Francisco, California, United States of America
| | - Paul W. Collins
- Department of Vertebrate Zoology, Santa Barbara Museum of Natural History, Santa Barbara, California, United States of America
| | - Tim Coonan
- National Park Service, Channel Islands National Park, Ventura, California, United States of America
| | - Julie L. King
- Catalina Island Conservancy, Avalon, California, United States of America
| | - Scott A. Morrison
- The Nature Conservancy, San Francisco, California, United States of America
| | - Seth D. Newsome
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - T. Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
| | - Jesus E. Maldonado
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, United States of America
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
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Semenova AV, Stroganov AN, Afanasiev KI, Rubtsova GA. Population structure and variability of Pacific herring (Clupea pallasii) in the White Sea, Barents and Kara Seas revealed by microsatellite DNA analyses. Polar Biol 2015; 38:951-65. [DOI: 10.1007/s00300-015-1653-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abstract
SSR genotyping involves the use of simple sequence repeats (SSRs) as DNA markers. SSRs, also called microsatellites, are a type of repetitive DNA sequence ubiquitous in most plant genomes. SSRs contain repeats of a motif sequence 1-6 bp in length. Due to this structure SSRs frequently undergo mutations, mainly due to DNA polymerase errors, which involve the addition or subtraction of a repeat unit. Hence, SSR sequences are highly polymorphic and may be readily used for detection of allelic variation within populations. SSRs are present within both genic and nongenic regions and are occasionally transcribed, and hence may be identified in expressed sequence tags (ESTs) as well as more commonly in nongenic DNA sequences. SSR genotyping involves the design of DNA-based primers to amplify SSR sequences from extracted genomic DNA, followed by amplification of the SSR repeat region using polymerase chain reaction, and subsequent visualization of the resulting DNA products, usually using gel electrophoresis. These procedures are described in this chapter. SSRs have been one of the most favored molecular markers for plant genotyping in the last 20 years due to their high levels of polymorphism, wide distribution across most plant genomes, and ease of use and will continue to be a useful tool in many species for years to come.
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Affiliation(s)
- Annaliese S Mason
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia,
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Kamat N, Khidhir MA, Hussain S, Alashari MM, Rannug U. Chemotherapy induced microsatellite instability and loss of heterozygosity in chromosomes 2, 5, 10, and 17 in solid tumor patients. Cancer Cell Int 2014; 14:118. [PMID: 25493073 PMCID: PMC4260186 DOI: 10.1186/s12935-014-0118-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/27/2014] [Indexed: 01/05/2023] Open
Abstract
Background The inevitable side effects of the currently used chemotherapy are associated with serious syndromes. Genotoxic effects and consequent genetic instability may play an important role in these syndromes. The aim of the study was to evaluate chemotherapy-related microsatellite instability (MSI), loss of heterozygosity (LOH), and loss of mismatch repair (MMR) expression in solid tumor patients. Methods Samples were collected from 117 de novo patients with solid tumors of different origins. Specimens, taken pre- and post-treatment, were screened for MSI and LOH in 10 microsatellite sequences in blood, and expression of five MMR proteins were analyzed in cancer tissues using immunohistochemistry. Statistical analysis included the use of; Fisher’s exact test, Chi Square, and an inter-rater reliability test using Cohen’s kappa coefficient. Results Microsatellite analysis showed that 66.7% of the patients had MSI, including 23.1% high-positive MSI and 43.6% low-positive MSI. A large portion (41%) of the patients exhibited LOH in addition to MSI. MSI and LOH were detected in seven loci in which incidence rates ranged from 3.8% positive for Bat-26 to 34.6% positive for Tp53-Alu. Immunohistochemistry revealed that human mutL homolog 1 (hMLH1) expression was deficient in 29.1% of the patients, whereas 18.8%, 23.9%, 13.4%, and 9.7% were deficient for human mutS homolog 2 (hMSH2), P53, human mutS homolog 6 (hMSH6) and human post-meiotic segregation increased 2 (hPMS2), respectively. There was a significant correlation between MSI and LOH incidence in Tp53-Alu, Mfd41, and APC with low or deficient expression of hMLH1, hMSH2, and P53. A significant association between MSI and LOH, and incidence of secondary tumors was also evident. Conclusions The negative correlation between MMR expression, MSI, and LOH and increased resistance to anti-cancer drugs and development of secondary cancers demonstrates a useful aid in early detection of potential chemotherapy-related side-effects. The diagnostic value demonstrated in our earlier study on breast cancer patients was confirmed for other solid tumors. Electronic supplementary material The online version of this article (doi:10.1186/s12935-014-0118-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nasir Kamat
- Department of Molecular Biosciences, the Wenner-Gren Institute (MBW), Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mohammed A Khidhir
- Department of Genetics Research, Management of Natural Conservations, AlAin City, UAE
| | - Sabir Hussain
- Department of Oncology and Hematology, Tawam Hospital, AlAin City, UAE
| | - Mouied M Alashari
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112 USA
| | - Ulf Rannug
- Department of Molecular Biosciences, the Wenner-Gren Institute (MBW), Stockholm University, SE-106 91 Stockholm, Sweden
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Zia ZU, Sadaqat HA, Tahir MHN, Sadia B, Bushman BS, Hole D, Michaels L, Malik W. Estimation of genetic diversity using SSR markers in sunflower. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414050147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kamler JF, Gray MM, Oh A, Macdonald DW. Genetic structure, spatial organization, and dispersal in two populations of bat-eared foxes. Ecol Evol 2013; 3:2892-902. [PMID: 24101981 PMCID: PMC3790538 DOI: 10.1002/ece3.683] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 11/07/2022] Open
Abstract
We incorporated radio-telemetry data with genetic analysis of bat-eared foxes (Otocyon megalotis) from individuals in 32 different groups to examine relatedness and spatial organization in two populations in South Africa that differed in density, home-range sizes, and group sizes. Kin clustering occurred only for female dyads in the high-density population. Relatedness was negatively correlated with distance only for female dyads in the high-density population, and for male and mixed-sex dyads in the low-density population. Home-range overlap of neighboring female dyads was significantly greater in the high compared to low-density population, whereas overlap within other dyads was similar between populations. Amount of home-range overlap between neighbors was positively correlated with genetic relatedness for all dyad-site combinations, except for female and male dyads in the low-density population. Foxes from all age and sex classes dispersed, although females (mostly adults) dispersed farther than males. Yearlings dispersed later in the high-density population, and overall exhibited a male-biased dispersal pattern. Our results indicated that genetic structure within populations of bat-eared foxes was sex-biased, and was interrelated to density and group sizes, as well as sex-biases in philopatry and dispersal distances. We conclude that a combination of male-biased dispersal rates, adult dispersals, and sex-biased dispersal distances likely helped to facilitate inbreeding avoidance in this evolutionarily unique species of Canidae.
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Affiliation(s)
- Jan F Kamler
- Wildlife Conservation Research Unit, Department of Zoology, The Recanati-Kaplan Centre, University of Oxford Tubney House, Abingdon Road, Tubney, Abingdon, OX13 5QL, UK
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Abstract
Small, isolated populations may experience increased extinction risk due to reduced genetic variability at important functional genes, thus decreasing the population's adaptive potential. The major histocompatibility complex (MHC), a key immunological gene cluster, usually shows high variability maintained by positive or balancing selection in response to challenges by pathogens. Here we investigated for the first time, the variability of 3 MHC class II genes (DRB1, DQA1, and DQB1) in 94 samples collected from Italian wolves. The Italian wolf population has been long isolated south of the Alps and is presently recovering from a recent bottleneck that decreased the population to less than 100 individuals. Despite the bottleneck, Italian wolves show remarkable MHC variability with 6-9 alleles per locus, including 2 recently described alleles at DRB1. MHC sequences show signatures of historical selective pressures (high d N/d S ratio, ω > 1.74) but no evidence of ongoing selection. Variation at the MHC genes and 12 background microsatellite loci were not apparently affected by the recent bottleneck. Although MHC alleles of domestic dog origin were detected in 8 genetically admixed individuals, these alleles were rare or absent in nonadmixed wolves. Thus, despite known hybridization events between domestic dogs and Italian wolves, the Italian wolf population does not appear affected by deep introgression of domestic dog MHC alleles.
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Affiliation(s)
- Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale, Ozzano dell’Emilia, Bologna, Italy.
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Vences M, Hauswaldt JS, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Mol Phylogenet Evol 2013; 68:657-70. [PMID: 23632031 DOI: 10.1016/j.ympev.2013.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
Abstract
We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
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Duca M, Port A, Şestacova T, Siniauskaya M, Aksyonova E, Davydenko O. Microsatellite Marker Application in Sunflower ( Helianthus AnnuusL.) Fingerprinting. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Kessler D, Bhattacharya S, Diezel C, Rothe E, Gase K, Schöttner M, Baldwin IT. Unpredictability of nectar nicotine promotes outcrossing by hummingbirds in Nicotiana attenuata. Plant J 2012; 71:529-38. [PMID: 22448647 DOI: 10.1111/j.1365-313x.2012.05008.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Many plants use sophisticated strategies to maximize their reproductive success via outcrossing. Nicotiana attenuata flowers produce nectar with nicotine at concentrations that are repellent to hummingbirds, increasing the number of flowers visited per plant. In choice tests using native hummingbirds, we show that these important pollinators learn to tolerate high-nicotine nectar but prefer low-nicotine nectar, and show no signs of nicotine addiction. Nectar nicotine concentrations, unlike those of other vegetative tissues, are unpredictably variable among flowers, not only among populations, but also within populations, and even among flowers within an inflorescence. To evaluate whether variations in nectar nicotine concentrations increase outcrossing, polymorphic microsatellite markers, optimized to evaluate paternity in native N. attenuata populations, were used to compare outcrossing in plants silenced for expression of a biosynthetic gene for nicotine production (Napmt1/2) and in control empty vector plants, which were antherectomized and transplanted into native populations. When only exposed to hummingbird pollinators, seeds produced by flowers with nicotine in their nectar had a greater number of genetically different sires, compared to seeds from nicotine-free flowers. As the variation in nectar nicotine levels among flowers in an inflorescence decreased in N. attenuata plants silenced in various combinations of three Dicer-like (DCL) proteins, small RNAs are probably involved in the unpredictable variation in nectar nicotine levels within a plant.
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Affiliation(s)
- Danny Kessler
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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Abstract
Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.
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Affiliation(s)
- Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada.
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Li J, Jin Z, Tan T. Genetic diversity and differentiation of Sinocalycanthus chinensis populations revealed by chloroplast microsatellite (cpSSRs) markers. BIOCHEM SYST ECOL 2012; 41:48-54. [DOI: 10.1016/j.bse.2011.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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García K, Gavilán RG, Höfle MG, Martínez-Urtaza J, Espejo RT. Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions. PLoS One 2012; 7:e30823. [PMID: 22292049 PMCID: PMC3265528 DOI: 10.1371/journal.pone.0030823] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 12/22/2011] [Indexed: 11/18/2022] Open
Abstract
The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10(-4) mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered.
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Affiliation(s)
- Katherine García
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Ronnie G. Gavilán
- Instituto de Acuicultura, Universidad de Santiago de Compostela, Campus Universitario Sur, Santiago de Compostela, Spain
| | - Manfred G. Höfle
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Jaime Martínez-Urtaza
- Instituto de Acuicultura, Universidad de Santiago de Compostela, Campus Universitario Sur, Santiago de Compostela, Spain
| | - Romilio T. Espejo
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- * E-mail:
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Sutton JT, Nakagawa S, Robertson BC, Jamieson IG. Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes. Mol Ecol 2011; 20:4408-20. [PMID: 21981032 DOI: 10.1111/j.1365-294x.2011.05292.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jolene T Sutton
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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Boto L, Cunha C, Doadrio I. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids. Genet Mol Biol 2011; 34:524-8. [PMID: 21931529 PMCID: PMC3168197 DOI: 10.1590/s1415-47572011005000023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 03/23/2011] [Indexed: 11/22/2022] Open
Abstract
A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose..
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Affiliation(s)
- Luis Boto
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales, CSIC, Madrid, Spain
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Floyd CH, Van Vuren DH, Crooks KR, Jones KL, Garcelon DK, Belfiore NM, Dragoo JW, May B. Genetic differentiation of island spotted skunks,Spilogale gracilis amphiala. J Mammal 2011. [DOI: 10.1644/09-mamm-a-204.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Fourie G, Steenkamp ET, Ploetz RC, Gordon TR, Viljoen A. Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex. Infect Genet Evol 2011; 11:533-42. [PMID: 21256980 DOI: 10.1016/j.meegid.2011.01.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 01/12/2011] [Accepted: 01/14/2011] [Indexed: 12/24/2022]
Abstract
Fusarium oxysporum is an asexual fungal species that includes human and animal pathogens and a diverse range of nonpathogens. Pathogenic and nonpathogenic strains of this species can be distinguished from each other with pathogenicity tests, but not with morphological analysis or sexual compatibility studies. Substantial genetic diversity among isolates has led to the realization that F. oxysporum represents a complex of cryptic species. F. oxysporum f. sp cubense (Foc), causal agent of Fusarium wilt of banana, is one of the more than 150 plant pathogenic forms of F. oxysporum. Multi-gene phylogenetic studies of Foc revealed at least eight phylogenetic lineages, a finding that was supported by random amplified polymorphic DNAs, restriction fragment length polymorphisms and amplified fragment length polymorphisms. Most of these lineages consist of isolates in closely related vegetative compatibility groups, some of which possess opposite mating type alleles, MAT-1 and MAT-2; thus, the evolutionary history of this fungus may have included recent sexual reproduction. The ability to cause disease on all or some of the current race differential cultivars has evolved convergently in the taxon, as members of some races appear in different phylogenetic lineages. Therefore, various factors including co-evolution the plant host and horizontal gene transfer are thought to have shaped the evolutionary history of Foc. This review discusses the evolution of Foc as a model formae specialis in F. oxysporum in relation to recent research findings involving DNA-based studies.
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Affiliation(s)
- G Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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Caliebe A, Jochens A, Krawczak M, Rösler U. A Markov chain description of the stepwise mutation model: Local and global behaviour of the allele process. J Theor Biol 2010; 266:336-42. [DOI: 10.1016/j.jtbi.2010.06.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 11/25/2022]
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Abstract
Detailed knowledge about the geographical pathways followed by propagules from their source to the invading populations--referred to here as routes of invasion-provides information about the history of the invasion process and the origin and genetic composition of the invading populations. The reconstruction of invasion routes is required for defining and testing different hypotheses concerning the environmental and evolutionary factors responsible for biological invasions. In practical terms, it facilitates the design of strategies for controlling or preventing invasions. Most of our knowledge about the introduction routes of invasive species is derived from historical and observational data, which are often sparse, incomplete and, sometimes, misleading. In this context, population genetics has proved a useful approach for reconstructing routes of introduction, highlighting the complexity and the often counterintuitive nature of the true story. This approach has proved particularly useful since the recent development of new model-based methods, such as approximate Bayesian computation, making it possible to make quantitative inferences in the complex evolutionary scenarios typically encountered in invasive species. In this review, we summarize some of the fundamental aspects of routes of invasion, explain why the reconstruction of these routes is useful for addressing both practical and theoretical questions, and comment on the various reconstruction methods available. Finally, we consider the main insights obtained to date from studies of invasion routes.
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Affiliation(s)
- Arnaud Estoup
- INRA UMR Centre de Biologie et de Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro), Campus international de Baillarguet, Montferrier-sur-Lez 34988, FranceEquipe 'Biologie des Populations en Interaction', UMR 1301 IBSV INRA-CNRS-Université de Nice-Sophia Antipolis 400 route des Chappes, 06903 Sophia-Antipolis Cedex, France
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Segarra A, Pépin JF, Arzul I, Morga B, Faury N, Renault T. Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008. Virus Res 2010; 153:92-9. [PMID: 20638433 DOI: 10.1016/j.virusres.2010.07.011] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 07/08/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
Ostreid herpesvirus 1 (OsHV-1) infections have been reported around the world and are associated with high mortalities of the Pacific oyster (Crassostrea gigas). In the summer 2008, abnormal mortality rates ranging from 80% to 100% were reported in France and affected only Pacific oysters. Analyses of oyster samples collected during mortality outbreaks demonstrated a significant detection of OsHV-1 (75% of analysed batches), which appeared stronger than previous years. DNA sequencing based on C and IA regions was carried out on 28 batches of OsHV-1 infected Pacific oysters collected in 2008. Polymorphisms were described in both the C and IA regions and characterized a genotype of OsHV-1 not already reported and termed OsHV-1 microVar. A microsatellite zone present in the C region showed several deletions. Additionally, 44 isolates collected in France and in the USA, from 1995 to 2007 were sequenced and compared to the 2008 sequences. The analyses of 76 sequences showed OsHV-1 microVar detection only in 2008 isolates. These data suggest that OsHV-1 microVar can be assumed as an emergent genotype.
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Affiliation(s)
- Amélie Segarra
- Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie (LGP), Avenue de Mus de Loup, 17390 La Tremblade, France
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Wright HWY, Gray MM, Wayne RK, Woodroffe RB. Mating tactics and paternity in a socially monogamous canid, the bat-eared fox (Otocyon megalotis). J Mammal 2010. [DOI: 10.1644/09-mamm-a-046.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lee T, Zenger KR, Close RL, Jones M, Phalen DN. Defining spatial genetic structure and management units for vulnerable koala (Phascolarctos cinereus) populations in the Sydney region, Australia. Wildl Res 2010. [DOI: 10.1071/wr09134] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context. Mammal populations around the world are increasingly threatened with population fragmentation because of loss of habitat or barriers to gene flow. The investigation of koala populations in the Sydney region not only provides valuable information about this vulnerable species, but also serves as a model for other species that have suffered major rapid declines in population size, and are now recovering in fragmented habitat. The peri-urban study region allows investigation of the impact of landscape features such as major roads and housing developments on koala gene flow. Aims. Animals originating from four geographic sampling areas around Sydney, New South Wales, Australia, were examined to determine population structure and gene flow and to identify barriers to gene flow and management units. Methods. The present study examined 12 microsatellite loci and used Bayesian assignment methods and genic frequency analysis methods to identify demographically separate populations and barriers to gene flow between those populations. Key results. Three discrete populations were resolved, with all displaying moderate to high levels of genetic differentiation among them (θ = 0.141–0.224). The allelic richness and heterozygosity of the Blue Mountains population (A = 6.46, HO = 0.66) is comparable to the highest diversity found in any koala population previously investigated. However, considerably lower genetic diversity was found in the Campbelltown population (A = 3.17, HO = 0.49), which also displayed evidence of a recent population bottleneck (effective population size estimated at 16–21). Conclusions. Animals separated by a military reserve were identified as one population, suggesting that the reserve maintains gene flow within this population. By contrast, strong differentiation of two geographically close populations separated by several potential barriers to gene flow suggested these land-use features pose barriers to gene flow. Implications. Implications of these findings for management of koala populations in the Greater Sydney region are discussed. In particular, the need to carefully consider the future of a military reserve is highlighted, along with possible solutions to allow gene flow across the proposed barrier regions. Because these are demographically separate populations, specific management plans tailored to the needs of each population will need to be formulated.
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Guillemaud T, Beaumont MA, Ciosi M, Cornuet J, Estoup A. Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data. Heredity (Edinb) 2010; 104:88-99. [DOI: 10.1038/hdy.2009.92] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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POSTMA ERIK, DEN TEX ROBERTJAN, VAN NOORDWIJK ARIEJ, MATEMAN ACHRISTA. Neutral markers mirror small-scale quantitative genetic differentiation in an avian island population. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01252.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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SCHUTZ HEIDI, POLLY PDAVID, KRIEGER JONATHAND, GURALNICK ROBERTP. Differential sexual dimorphism: size and shape in the cranium and pelvis of grey foxes (Urocyon). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01132.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Desde la óptica de la diversidad genética, Colombia es un país megadiverso con variabilidad ecosistémica importante, la cual puede ser aprovechada para el desarrollo de sistemas de producción sostenibles, eficientes y competitivos. Esto implica, aparte de la conservación de los recursos genéticos estratégicos vegetales, animales y de microorganismos, conocer el potencial de esta agrobiodiversidad para su utilización amplia, con apoyo de procesos convencionales y de la biotecnología moderna, que permitan proveer alimentos y el desarrollo del concepto integral del manejo de agroecosistemas. Por ello, en la revisión actual se incluye una descripción de la importancia de la diversidad biológica agrícola, en el nuevo contexto mundial y la necesidad de realizar procesos de conocimiento de la variabilidad y los atributos presentes en ésta, para trasladar el recurso genético de valor de existencia a los de opción y utilización.
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McFadden KW, Gompper ME, Valenzuela DG, Morales JC. Evolutionary history of the critically endangered Cozumel dwarf carnivores inferred from mitochondrial DNA analyses. J Zool (1987) 2008. [DOI: 10.1111/j.1469-7998.2008.00461.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gao LZ, Xu H. Comparisons of mutation rate variation at genome-wide microsatellites: evolutionary insights from two cultivated rice and their wild relatives. BMC Evol Biol 2008; 8:11. [PMID: 18199337 PMCID: PMC2241587 DOI: 10.1186/1471-2148-8-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 01/16/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutation rate (mu) per generation per locus is an important parameter in the models of population genetics. Studies on mutation rate and its variation are of significance to elucidate the extent and distribution of genetic variation, further infer evolutionary relationships among closely related species, and deeply understand genetic variation of genomes. However, patterns of rate variation of microsatellite loci are still poorly understood in plant species. Furthermore, how their mutation rates vary in di-, tri-, and tetra-nucleotide repeats within the species is largely uninvestigated across related plant genomes. RESULTS Genome-wide variation of mutation rates was first investigated by means of the composite population parameter theta (theta = 4Nmu, where N is the effective population size and mu is the mutation rate per locus per generation) in four subspecies of Asian cultivated rice O. sativa and its three related species, O. rufipogon, O. glaberrima, and O. officinalis. On the basis of three data sets of microsatellite allele frequencies throughout the genome, population mutation rate (theta) was estimated for each locus. Our results reveal that the variation of population mutation rates at microsatellites within each studied species or subspecies of cultivated rice can be approximated with a gamma distribution. The mean population mutation rates of microsatellites do not significantly differ in motifs of di-, tri-, and tetra-nucleotide repeats for the studied rice species. The shape parameter was also estimated for each subspecies of rice as well as other related rice species. Of them, different subspecies of O. sativa possesses similar shape parameters (alpha) of the gamma distribution, while other species extensively vary in their population mutation rates. CONCLUSION Through the analysis of genome-wide microsatellite data, the population mutation rate can be approximately fitted with a gamma distribution in most of the studied species. In general, different population histories occurred along different lineages may result in the observed variation of population mutation rates at microsatellites among the studied Oryza species.
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Affiliation(s)
- Li-Zhi Gao
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650204, PR China.
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Gonzalez EG, Zardoya R. Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus). BMC Evol Biol 2007; 7:197. [PMID: 17953768 PMCID: PMC2204010 DOI: 10.1186/1471-2148-7-197] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 10/22/2007] [Indexed: 12/04/2022] Open
Abstract
Background Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (S. p. pilchardus and S. p. sardina). Results We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and RST pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test. Conclusion We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.
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Affiliation(s)
- Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2; 28006 Madrid, Spain.
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Bollmer JL, Vargas FH, Parker PG. Low MHC variation in the endangered Galápagos penguin (Spheniscus mendiculus). Immunogenetics 2007; 59:593-602. [PMID: 17457582 DOI: 10.1007/s00251-007-0221-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 03/31/2007] [Indexed: 10/23/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most polymorphic regions of the genome, likely due to balancing selection acting to maintain alleles over time. Lack of MHC variability has been attributed to factors such as genetic drift in small populations and relaxed selection pressure. The Galápagos penguin (Spheniscus mendiculus), endemic to the Galápagos Islands, is the only penguin that occurs on the equator. It relies upon cold, nutrient-rich upwellings and experiences severe population declines when ocean temperatures rise during El Niño events. These bottlenecks, occurring in an already small population, have likely resulted in reduced genetic diversity in this species. In this study, we used MHC class II exon 2 sequence data from a DRB1-like gene to characterize the amount of genetic variation at the MHC in 30 Galápagos penguins, as well as one Magellanic penguin (S. magellanicus) and two king penguins (Aptenodytes patagonicus), and compared it to that in five other penguin species for which published data exist. We found that the Galápagos penguin had the lowest MHC diversity (as measured by number of polymorphic sites and average divergence among alleles) of the eight penguin species studied. A phylogenetic analysis showed that Galápagos penguin MHC sequences are most closely related to Humboldt penguin (Spheniscus humboldti) sequences, its putative sister species based on other loci. An excess of non-synonymous mutations and a pattern of trans-specific evolution in the neighbor-joining tree suggest that selection is acting on the penguin MHC.
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Affiliation(s)
- Jennifer L Bollmer
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA.
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Grubisha LC, Bergemann SE, Bruns TD. Host islands within the California Northern Channel Islands create fine-scale genetic structure in two sympatric species of the symbiotic ectomycorrhizal fungus Rhizopogon. Mol Ecol 2007; 16:1811-22. [PMID: 17444894 DOI: 10.1111/j.1365-294x.2007.03264.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have examined fine-scale genetic structure of the symbiotic ectomycorrhizal fungi Rhizopogon occidentalis and R. vulgaris on two of the California Channel Islands using five and six microsatellite loci, respectively. Both Rhizopogon species are sympatric on Santa Cruz and Santa Rosa Islands and are ectomycorrhizal with bishop pine (Pinus muricata) on both islands or Santa Rosa Island Torrey pine (P. torreyana ssp. insularis) on Santa Rosa. The combination of disjunct pine host distributions and geographic barriers within and among the islands have created highly structured Rhizopogon populations over very short distances (8.5 km on Santa Cruz Island; F(ST) = 0.258, F(ST) = 0.056, R. occidentalis and R. vulgaris, respectively). Both species show similar patterns of genetic differentiation as a result of limited dispersal between host populations as revealed by a significant isolation by distance relationship (r = 0.69, P < 0.04; r = 0.93, P < 0.001, R. occidentalis and R. vulgaris, respectively) and Bayesian clustering analyses, and is most likely a function of the small foraging range of the few mammals that disperse Rhizopogon on these islands and the enormous spore bank characteristic of Rhizopogon species.
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Affiliation(s)
- Lisa C Grubisha
- Department of Plant and Microbial Biology, 111 Koshland, University of California, Berkeley, CA 94720-3102, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.
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Affiliation(s)
- Marta Barluenga
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Abstract
Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.
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Affiliation(s)
- Raphael Leblois
- Laboratoire Génétique et Environnement, CNRS-UMR 5554, 34095 Montpellier, France
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Affiliation(s)
- M. E. Gompper
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO, USA
| | - A. E. Petrites
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO, USA
| | - R. L. Lyman
- Department of Anthropology, University of Missouri, Columbia, MO, USA
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