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Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak ( Quercus cerris L.). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010018. [PMID: 36675965 PMCID: PMC9863001 DOI: 10.3390/life13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/02/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by FST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy.
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Yakimowski SB, Southcott L, Barrett SCH. Contrasting patterns of genetic diversity and differentiation across the continental disjunct range of a sexually polymorphic aquatic plant. ANNALS OF BOTANY 2022; 130:27-40. [PMID: 35511701 PMCID: PMC9295920 DOI: 10.1093/aob/mcac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/28/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Reproductive systems enabling opportunities for self-fertilization influence population genetic structure and play a key role in colonization and genetic differentiation during range expansion. Because of their well-developed powers of dispersal, aquatic plants often have widespread disjunct geographical distributions, providing opportunities to investigate the role of reproductive systems in structuring genetic variation between parts of the range that differ in migration history and ecology. METHODS We compared reproductive systems and spatial genetic structure of the freshwater aquatic macrophyte Sagittaria latifolia between disjunct western and eastern ranges of North America (NA). Populations of this species are most commonly either monoecious or dioecious. We examined chloroplast DNA haplotype variation to test the hypothesis that the western range of this species represents a secondary colonization from the east, and evaluated the roles of reproductive system differences and geography in structuring contemporary patterns of genetic variation at 11 polymorphic SSR (simple sequence repeat) loci. KEY RESULTS Chloroplast haplotyping revealed a single haplotype in western NA compared to numerous haplotypes in eastern NA, consistent with a genetic bottleneck during westward migration. Estimates of genetic diversity in eastern NA populations differed significantly between reproductive systems, but this pattern was not evident in the western range. Eastern populations could be reliably assigned to genetic clusters based on their reproductive systems, whereas western populations clustered primarily by geographical location. CONCLUSIONS The sparser distribution of aquatic habitats in the drier western range of S. latifolia, combined with secondary colonization of this region, probably cause the lower genetic diversity and increased differentiation among populations, possibly overriding the effects of reproductive system evident in the eastern portion of the range. Our findings demonstrate that the complex interplay between migratory history, reproductive systems and habitat availability plays an important role in structuring spatial patterns of genetic variation in disjunct plant populations.
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Affiliation(s)
| | - Laura Southcott
- Department of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, ON, Canada
- Committee on Evolutionary Biology, Chicago, IL, USA
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, ON, Canada
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Mustafa MSEK, Jaal Z, Abu Kashawa S, Mohd Nor SA. Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan. Malar J 2021; 20:469. [PMID: 34923983 PMCID: PMC8684682 DOI: 10.1186/s12936-021-03994-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.
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Affiliation(s)
| | - Zairi Jaal
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Sumia Abu Kashawa
- Faculty of Science, Department of Zoology, University of Khartoum, Khartoum, Sudan
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
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4
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Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction. Sci Rep 2020; 10:19112. [PMID: 33154411 PMCID: PMC7644706 DOI: 10.1038/s41598-020-76092-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/22/2020] [Indexed: 11/08/2022] Open
Abstract
Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.
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Hanna ZR, Cicero C, Bowie RCK. Molecular evidence that the Channel Islands populations of the orange-crowned warbler ( Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage. PeerJ 2019; 7:e7388. [PMID: 31404458 PMCID: PMC6688592 DOI: 10.7717/peerj.7388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/01/2019] [Indexed: 11/23/2022] Open
Abstract
We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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6
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Putnová L, Štohl R. Comparing assignment-based approaches to breed identification within a large set of horses. J Appl Genet 2019; 60:187-198. [PMID: 30963515 DOI: 10.1007/s13353-019-00495-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
Abstract
Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highest genetic divergence (FST = 0.378) was established between the Friesian and Equus przewalskii; the highest degree of gene migration was obtained between the Czech and Bavarian Warmblood (Nm = 14,302); and the overall global heterozygote deficit across the populations was 10.4%. The eight standard methods (Bayesian, frequency, and distance) using GeneClass software and almost all mainstream classification algorithms (Bayes Net, Naive Bayes, IB1, IB5, KStar, JRip, J48, Random Forest, Random Tree, PART, MLP, and SVM) from the WEKA machine learning workbench were compared by utilizing 314,874 real allelic data sets. The Bayesian method (GeneClass, 89.9%) and Bayesian network algorithm (WEKA, 84.8%) outperformed the other techniques. The breed genomic prediction accuracy reached the highest value in the cold-blooded horses. The overall proportion of individuals correctly assigned to a population depended mainly on the breed number and genetic divergence. These statistical tools could be used to assess breed traceability systems, and they exhibit the potential to assist managers in decision-making as regards breeding and registration.
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Affiliation(s)
- Lenka Putnová
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1665/1, 613 00, Brno, Czech Republic.
| | - Radek Štohl
- Department of Control and Instrumentation, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3082/12, 616 00, Brno, Czech Republic
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Farris E, Filigheddu R, Mameli G, Falanga V, Vanetti I, Rosati L, Binelli G. Is population genetic structure of vascular plants shaped more by ecological or geographic factors? A study case on the Mediterranean endemic Centaurea filiformis (Asteraceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:936-947. [PMID: 29873892 DOI: 10.1111/plb.12853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
All known populations of the Sardinian endemic Centaurea filiformis Viv. (Asteraceae) were studied in order to understand the impact of both geographic and ecological factors on the genetic structuring of this species. Fourteen populations and 234 individuals were sampled. The demographic structure of the populations and the reproductive ecology were estimated in 28 plots. Population genetic analyses were based on SSR markers. Genetic structure was investigated by spatial Bayesian methods. Average densities of 0.51 individuals m-2 were detected, with a prevalence of adults. Ten species of pollinators were identified; C. filiformis ability to self-pollinate and myrmecochory were demonstrated experimentally. The populations displayed an average heterozygosity value of He = 0.576 and high genetic differentiation (overall FST = 0.218). Bayesian analysis suggests that five is the most probable number of gene pools of origin. A strong correlation between geographic distances and genetic distances among populations was highlighted. The demographic population structure of C. filiformis is dominated by adults, suggesting that it is a stable-regressive or senile species, investing more in local persistence than colonisation ability. Despite the scattered distribution, the populations studied do not present evidence of genetic erosion. The analysis of genetic differentiation reveals very high differentiation levels among populations, thus indicating that effective barriers exist against gene flow. A general conclusion is that population distribution results in a clear genetic structure for the populations studied, and that geography and not ecology is shaping the present distribution of this species.
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Affiliation(s)
- E Farris
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - R Filigheddu
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - G Mameli
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - V Falanga
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
| | - I Vanetti
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
| | - L Rosati
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - G Binelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
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8
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Mora MS, Mapelli FJ, López A, Gómez Fernández MJ, Mirol PM, Kittlein MJ. Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina. Genetica 2017; 145:575-591. [PMID: 28905157 DOI: 10.1007/s10709-017-9983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 09/07/2017] [Indexed: 11/29/2022]
Abstract
Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.
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Affiliation(s)
- Matías Sebastián Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina.
| | - Fernando J Mapelli
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
| | - Aldana López
- Área de Recursos Naturales, CONICET INTA EEA Bariloche, CC 277 8400, Bariloche, Río Negro, Argentina
| | - María Jimena Gómez Fernández
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Patricia M Mirol
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
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Wilmer JW, Hall L, Barratt E, Moritz C. GENETIC STRUCTURE AND MALE-MEDIATED GENE FLOW IN THE GHOST BAT (MACRODERMA GIGAS). Evolution 2017; 53:1582-1591. [PMID: 28565551 DOI: 10.1111/j.1558-5646.1999.tb05421.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/1998] [Accepted: 04/26/1999] [Indexed: 11/29/2022]
Abstract
The Australian ghost bat is a large, opportunistic carnivorous species that has undergone a marked range contraction toward more mesic, tropical sites over the past century. Comparison of mitochondrial DNA (mtDNA) control region sequences and six nuclear microsatellite loci in 217 ghost bats from nine populations across subtropical and tropical Australia revealed strong population subdivision (mtDNA φST = 0.80; microsatellites URST = 0.337). Low-latitude (tropical) populations had higher heterozygosity and less marked phylogeographic structure and lower subdivision among sites within regions (within Northern Territory [NT] and within North Queensland [NQ]) than did populations at higher latitudes (subtropical sites; central Queensland [CQ]), although sampling of geographically proximal breeding sites is unavoidably restricted for the latter. Gene flow among populations within each of the northern regions appears to be male biased in that the difference in population subdivision for mtDNA and microsatellites (NT φST = 0.39, URST = 0.02; NQ φST = 0.60, URST = -0.03) is greater than expected from differences in the effective population size of haploid versus diploid loci. The high level of population subdivision across the range of the ghost bat contrasts with evidence for high gene flow in other chiropteran species and may be due to narrow physiological tolerances and consequent limited availability of roosts for ghost bats, particularly across the subtropical and relatively arid regions. This observation is consistent with the hypothesis that the contraction of the species' range is associated with late Holocene climate change. The extreme isolation among higher-latitude populations may predispose them to additional local extinctions if the processes responsible for the range contraction continue to operate.
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Affiliation(s)
- Jessica Worthington Wilmer
- Department of Zoology and Entomology, University of Queensland, St. Lucia, Queensland, 4072, Australia.,Department of Anatomical Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Les Hall
- Department of Anatomical Sciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Elizabeth Barratt
- Conservation Genetics Group, Institute of Zoology, Regents Park, London, NW1 4RY, United Kingdom
| | - Craig Moritz
- Department of Zoology and Entomology, University of Queensland, St. Lucia, Queensland, 4072, Australia
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Lu G, Bernatchez L. CORRELATED TROPHIC SPECIALIZATION AND GENETIC DIVERGENCE IN SYMPATRIC LAKE WHITEFISH ECOTYPES (COREGONUS CLUPEAFORMIS): SUPPORT FOR THE ECOLOGICAL SPECIATION HYPOTHESIS. Evolution 2017; 53:1491-1505. [DOI: 10.1111/j.1558-5646.1999.tb05413.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/1998] [Accepted: 05/06/1999] [Indexed: 11/29/2022]
Affiliation(s)
- Guoqing Lu
- Département de biologie; GIROQ, Université Laval; Sainte-Foy Québec G1K 7P4 Canada
| | - Louis Bernatchez
- Département de biologie; GIROQ, Université Laval; Sainte-Foy Québec G1K 7P4 Canada
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11
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Bensch S, Andersson T, Åkesson S. MORPHOLOGICAL AND MOLECULAR VARIATION ACROSS A MIGRATORY DIVIDE IN WILLOW WARBLERS,PHYLLOSCOPUS TROCHILUS. Evolution 2017; 53:1925-1935. [DOI: 10.1111/j.1558-5646.1999.tb04573.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1998] [Accepted: 06/22/1999] [Indexed: 11/28/2022]
Affiliation(s)
- Staffan Bensch
- Department of Animal Ecology, Ecology Building; Lund University; S-223 62 Lund Sweden
| | - Tord Andersson
- Department of Animal Ecology, Ecology Building; Lund University; S-223 62 Lund Sweden
| | - Susanne Åkesson
- Department of Animal Ecology, Ecology Building; Lund University; S-223 62 Lund Sweden
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12
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Laggis A, Baxevanis AD, Charalampidou A, Maniatsi S, Triantafyllidis A, Abatzopoulos TJ. Microevolution of the noble crayfish (Astacus astacus) in the Southern Balkan Peninsula. BMC Evol Biol 2017; 17:122. [PMID: 28558646 PMCID: PMC5450353 DOI: 10.1186/s12862-017-0971-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 12/02/2022] Open
Abstract
Background The noble crayfish (Astacus astacus) displays a complex historical and contemporary genetic status in Europe. The species divergence has been shaped by geological events (i.e. Pleistocene glaciations) and humanly induced impacts (i.e. translocations, pollution, etc.) on its populations due to species commercial value and its niche degradation. Until now, limited genetic information has been procured for the Balkan area and especially for the southernmost distribution of this species (i.e. Greece). It is well known that the rich habitat diversity of the Balkan Peninsula offers suitable conditions for genetically diversified populations. Thus, the present manuscript revisits the phylogenetic relationships of the noble crayfish in Europe and identifies the genetic make-up and the biogeographical patterns of the species in its southern range limit. Results Mitochondrial markers (i.e. COI and 16S) were used in order to elucidate the genetic structure and diversity of the noble crayfish in Europe. Two of the six European haplotypic lineages, were found exclusively in Greece. These two lineages exhibited greater haplotypic richness when compared with the rest four (of “Central European” origin) while they showed high genetic diversity. Divergence time analysis identified that the majority of this divergence was captured through Pleistocene, suggesting a southern glacial refugium (Greece, southern Balkans). Furthermore, six microsatellite markers were used in order to define the factors affecting the genetic structure and demographic history of the species in Greece. The population structure analysis revealed six to nine genetic clusters and eight putative genetic barriers. Evidence of bottleneck effects in the last ~5000 years (due to climatic and geological events and human activities) is also afforded. Findings from several other research fields (e.g. life sciences, geology or even archaeology) have been utilized to perceive the genetic make-up of the noble crayfish. Conclusions The southernmost part of Balkans has played a major role as a glacial refugium for A. astacus. Such refugia have served as centres of expansion to northern regions. Recent history of the noble crayfish in southern Balkans reveals the influence of environmental (climate, geology and/or topology) and anthropogenic factors. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0971-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anastasia Laggis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Athanasios D Baxevanis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexandra Charalampidou
- Scientific Computing Office, Information Technology (IT) Center, School of Sciences, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Macedonia, Greece
| | - Stefania Maniatsi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexander Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Theodore J Abatzopoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
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Kurita K, Toda M. The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii). Genetica 2017; 145:223-234. [PMID: 28271307 DOI: 10.1007/s10709-017-9960-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/25/2017] [Indexed: 10/20/2022]
Abstract
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.
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Affiliation(s)
- Kazuki Kurita
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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Kimmel M, Wojdyła T. Genetic demographic networks: Mathematical model and applications. Theor Popul Biol 2016; 111:75-86. [PMID: 27378746 DOI: 10.1016/j.tpb.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans.
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Affiliation(s)
- Marek Kimmel
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA; Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
| | - Tomasz Wojdyła
- Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
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15
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Barros T, Ferreira E, Rocha RG, Gaubert P, Bandeira V, Souto L, Mira A, Fonseca C. Genetic signature of the northward expansion of the Egyptian mongoose Herpestes ichneumon(Herpestidae) in the Iberian Peninsula. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tânia Barros
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Eduardo Ferreira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Rita Gomes Rocha
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
- Departamento de Ciências Biológicas; Centro de Ciências Humanas e Naturais; Universidade Federal do Espírito Santo; Av. Fernando Ferrari 514, Goiabeiras 29075-910 Vitória ES Brazil
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-CIRAD-EPHE; Université de Montpellier; Place Eugène Bataillon - CC 64; 34095 Montpellier, Cedex 05 France
| | - Victor Bandeira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Luis Souto
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - António Mira
- Unidade de Biologia da Conservação; Universidade de Évora; 7002-554 Évora Portugal
| | - Carlos Fonseca
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
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16
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Omondi SF, Odee DW, Ongamo GO, Kanya JI, Khasa DP. Genetic consequences of anthropogenic disturbances and population fragmentation in Acacia senegal. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0854-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Tan MP, Jamsari AFJ, Siti Azizah MN. Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia. JOURNAL OF FISH BIOLOGY 2016; 88:1932-1948. [PMID: 27027270 DOI: 10.1111/jfb.12956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Genetic variability and differences in wild striped snakehead Channa striata from Malaysia were analysed by genotyping nine novel nuclear microsatellite loci. Analysis revealed moderate-to-high genetic diversity in most of the populations, indicative of large effective population sizes. The highly diversified populations are admixed populations and, therefore, can be recommended as potential candidates for selective breeding and conservation since they each contain most of the alleles found in their particular region. Three homogenous groups of the wild populations were identified, apparently separated by effective barriers, in accordance with contemporary drainage patterns. The highest population pairwise FST found between members of the same group reflects the ancient population connectivity; yet prolonged geographical isolation resulted in adaptation of alleles to local contemporary environmental change. A significant relationship between genetic distance and geographical isolation was observed (r = 0·644, P < 0·01). Anthropogenic perturbations indicated apparent genetic proximity between distant populations.
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Affiliation(s)
- M P Tan
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
- Institut Akuakultur Tropika (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - A F J Jamsari
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - M N Siti Azizah
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
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18
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Gene flow and fine-scale spatial genetic structure in Cabralea canjerana (Meliaceae), a common tree species from the Brazilian Atlantic forest. JOURNAL OF TROPICAL ECOLOGY 2016. [DOI: 10.1017/s0266467416000067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:The Atlantic forest is the biome most severely affected by deforestation in Brazil. Cabralea canjerana spp. canjerana is a dioecious tree species with widespread distribution in the Neotropical region. This species is considered a model to ascertain population ecology parameters for endangered plant species from the Atlantic forest. Fine-scale spatial genetic structure and pollen-mediated gene flow are crucial information in landscape genetics and evolutionary ecology. A total of 192 adults and 121 offspring were sampled in seven C. canjerana populations in the Southern Minas Gerais State, Brazil, to assess whether pollen-mediated gene flow is able to prevent spatial genetic structure within and among Atlantic forest fragments. Several molecular ecology parameters were estimated using microsatellite loci. High levels of genetic diversity (HE = 0.732) and moderate population structure (θ = 0.133) were recorded. No significant association between kinship and spatial distance amongst individuals within each population (Sp = 0.000109) was detected. Current pollen-mediated gene flow occurs mainly within forest fragments, probably due to short-distance flights of the pollinator of C. canjerana, and also the forest fragmentation may have restricted flight distance. The high levels of genetic differentiation found amongst the seven sites sampled demonstrated how habitat fragmentation affects the gene flow process in natural areas.
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19
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Souto CP, Kitzberger T, Arbetman MP, Premoli AC. How do cold-sensitive species endure ice ages? Phylogeographic and paleodistribution models of postglacial range expansion of the mesothermic drought-tolerant conifer Austrocedrus chilensis. THE NEW PHYTOLOGIST 2015; 208:960-972. [PMID: 26079667 DOI: 10.1111/nph.13508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/07/2015] [Indexed: 06/04/2023]
Abstract
In view of global climate change, it is important to understand the responses of tree species to climate changes in the past. Combinations of phylogeographic analysis of genetic evidence, coupled with species distribution models (SDMs), are improving our understanding on this subject. We combined SDMs and microsatellite data from populations of the entire range of Austrocedrus chilensis, a dominant mesotherm (cold-sensitive) conifer of dryland forests of the southern Andes, to test the hypothesis of long-distance postglacial migration from northern and warmer refugia at the Last Glacial Maximum (LGM). The SDM indicated suitable conditions for Austrocedrus in northern Chile (western) at the LGM and largely unsuitable conditions in Argentina (eastern). Population genetic diversity and effective population sizes within populations decreased southward along the Andes, consistent with the hypothesis of long-distance dispersal from a northern refugium. Results support the hypothesis of one (or a few) warmer (low latitude) refugia in Chile for Austrocedrus. On balance, the evidence suggests that in contrast to cold-tolerant tree taxa with the capacity to fast-track postglacial warming thanks to local refugia, cold-sensitive species might have undergone long-distance range expansion, lagging behind progressive climate change throughout the Holocene.
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Affiliation(s)
- Cintia P Souto
- Laboratorio Ecotono-INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Río Negro, Argentina
| | - Thomas Kitzberger
- Laboratorio Ecotono-INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Río Negro, Argentina
| | - Marina P Arbetman
- Laboratorio Ecotono-INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Río Negro, Argentina
- Universidad Nacional de Río Negro, Sede Andina, Bariloche, 8400, Río Negro, Argentina
| | - Andrea C Premoli
- Laboratorio Ecotono-INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, 8400, Río Negro, Argentina
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20
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Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island. PLoS One 2015; 10:e0138779. [PMID: 26488886 PMCID: PMC4619298 DOI: 10.1371/journal.pone.0138779] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 11/20/2022] Open
Abstract
The taxonomy of giant Galapagos tortoises (Chelonoidis spp.) is currently based primarily on morphological characters and island of origin. Over the last decade, compelling genetic evidence has accumulated for multiple independent evolutionary lineages, spurring the need for taxonomic revision. On the island of Santa Cruz there is currently a single named species, C. porteri. Recent genetic and morphological studies have shown that, within this taxon, there are two evolutionarily and spatially distinct lineages on the western and eastern sectors of the island, known as the Reserva and Cerro Fatal populations, respectively. Analyses of DNA from natural populations and museum specimens, including the type specimen for C. porteri, confirm the genetic distinctiveness of these two lineages and support elevation of the Cerro Fatal tortoises to the rank of species. In this paper, we identify DNA characters that define this new species, and infer evolutionary relationships relative to other species of Galapagos tortoises.
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21
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Cabria MT, Gonzalez EG, Gomez-Moliner BJ, Michaux JR, Skumatov D, Kranz A, Fournier P, Palazon S, Zardoya R. Patterns of genetic variation in the endangered European mink (Mustela lutreola L., 1761). BMC Evol Biol 2015; 15:141. [PMID: 26183103 PMCID: PMC4504092 DOI: 10.1186/s12862-015-0427-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/02/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The European mink (Mustela lutreola, L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing populations of this species, including new sampling sites and additional molecular markers (newly developed microsatellite loci specific to European mink) as compared to previous studies. Probabilistic analyses were used to examine genetic structure within and between existing populations, and to infer phylogeographic processes and past demography. RESULTS According to both mitochondrial and nuclear microsatellite markers, Northeastern (Russia, Estonia and Belarus) and Southeastern (Romania) European populations showed the highest intraspecific diversity. In contrast, Western European (France and Spain) populations were the least polymorphic, featuring a unique mitochondrial DNA haplotype. The high differentiation values detected between Eastern and Western European populations could be the result of genetic drift in the latter due to population isolation and reduction. Genetic differences among populations were further supported by Bayesian clustering and two main groups were confirmed (Eastern vs. Western Europe) along with two contained subgroups at a more local scale (Northeastern vs. Southeastern Europe; France vs. Spain). CONCLUSIONS Genetic data and performed analyses support a historical scenario of stable European mink populations, not affected by Quaternary climate oscillations in the Late Pleistocene, and posterior expansion events following river connections in both North- and Southeastern European populations. This suggests an eastern refuge during glacial maxima (as already proposed for boreal and continental species). In contrast, Western Europe was colonised more recently following either natural expansions or putative human introductions. Low levels of genetic diversity observed within each studied population suggest recent bottleneck events and stress the urgent need for conservation measures to counteract the demographic decline experienced by the European mink.
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Affiliation(s)
- Maria Teresa Cabria
- Departamento de Zoología y B.C.A., Facultad de Farmacia, Universidad del País Vasco UPV/EHU, Paseo de las Universidades, 7, 01006, Vitoria-Gasteiz, Spains.
- Laboratoire de Biologie Évolutive, Institut de Botanique (Bat.22), Université de Liège (Sart Tilman), Boulevard du Rectorat, 27, B4000, Liège, Belgium.
| | - Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
| | - Benjamin J Gomez-Moliner
- Departamento de Zoología y B.C.A., Facultad de Farmacia, Universidad del País Vasco UPV/EHU, Paseo de las Universidades, 7, 01006, Vitoria-Gasteiz, Spains.
| | - Johan R Michaux
- Laboratoire de Biologie Évolutive, Institut de Botanique (Bat.22), Université de Liège (Sart Tilman), Boulevard du Rectorat, 27, B4000, Liège, Belgium.
- Centre de Biologie et de Gestion des Populations, CBGP, Campus international de Baillarguet, CS 30016, 34988, Montferrier-sur-Lez, Cedex, France.
| | - Dimitry Skumatov
- Russian Research Institute of Game Management and Fur Farming, Engels Street, 79, Kirov, Russia.
| | - Andreas Kranz
- Institute of Wildlife Biology and Game Management, BOKU University of Natural Resources and Life Sciences, Gregor Mendel Street 33, 1180, Vienna, Austria.
| | - Pascal Fournier
- Groupe de Recherche et d'Etudes pour la Gestion de l'Environnement (GREGE), Route de Préchac, 33730, Villandraut, France.
| | - Santiago Palazon
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Diagonal 643, 2ª planta, 08028, Barcelona, Spain.
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
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22
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Cao LJ, Wen JB, Wei SJ, Liu J, Yang F, Chen M. Characterization of novel microsatellite markers for Hyphantria cunea and implications for other Lepidoptera. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:273-284. [PMID: 25772405 DOI: 10.1017/s0007485315000061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers for H. cunea from SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified as Grouped should not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy-Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, and F ST performed better than did R ST for the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies of H. cunea.
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Affiliation(s)
- L J Cao
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - J B Wen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - S J Wei
- Institute of Plant and Environmental Protection,Beijing Academy of Agriculture and Forestry Sciences,Beijing 100097,China
| | - J Liu
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - F Yang
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - M Chen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
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23
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Genetic and fitness consequences of interpopulation mating in Dianthus guliae Janka: conservation implications for severely depleted and isolated plant populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0727-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Garrick RC, Benavides E, Russello MA, Hyseni C, Edwards DL, Gibbs JP, Tapia W, Ciofi C, Caccone A. Lineage fusion in Galápagos giant tortoises. Mol Ecol 2014; 23:5276-90. [DOI: 10.1111/mec.12919] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Ryan C. Garrick
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
| | - Michael A. Russello
- Department of Biology; University of British Columbia; Okanagan Campus Kelowna BC V1V 1V7 Canada
| | - Chaz Hyseni
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
| | - Danielle L. Edwards
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
| | - James P. Gibbs
- College of Environmental Science & Forestry; State University of New York; Syracuse NY 13210 USA
| | - Washington Tapia
- Department of Applied Research; Galápagos National Park Service; Puerto Ayora Isla Santa Cruz Galápagos Ecuador
- Biodiver S.A. Consultores; Km 5 Vía a Baltra Isla Santa Cruz Galápagos Ecuador
| | - Claudio Ciofi
- Department of Evolutionary Biology; University of Florence; Via Romana 17 50125 Florence Italy
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT 06520 USA
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González C, Ornelas JF. Acoustic divergence with gene flow in a lekking hummingbird with complex songs. PLoS One 2014; 9:e109241. [PMID: 25271429 PMCID: PMC4182805 DOI: 10.1371/journal.pone.0109241] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/04/2014] [Indexed: 02/05/2023] Open
Abstract
Hummingbirds have developed a remarkable diversity of learned vocalizations, from single-note songs to phonologically and syntactically complex songs. In this study we evaluated if geographic song variation of wedge-tailed sabrewings (Campylopterus curvipennis) is correlated with genetic divergence, and examined processes that explain best the origin of intraspecific song variation. We contrasted estimates of genetic differentiation, genetic structure, and gene flow across leks from microsatellite loci of wedge-tailed sabrewings with measures for acoustic signals involved in mating derived from recordings of males singing at leks throughout eastern Mexico. We found a strong acoustic structure across leks and geography, where lek members had an exclusive assemblage of syllable types, differed in spectral and temporal measurements of song, and song sharing decreased with geographic distance. However, neutral genetic and song divergence were not correlated, and measures of genetic differentiation and migration estimates indicated gene flow across leks. The persistence of acoustic structuring in wedge-tailed sabrewings may thus best be explained by stochastic processes across leks, in which intraspecific vocal variation is maintained in the absence of genetic differentiation by postdispersal learning and social conditions, and by geographical isolation due to the accumulation of small differences, producing most dramatic changes between populations further apart.
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Affiliation(s)
- Clementina González
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, México
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, México
- * E-mail:
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Melo ATDO, Coelho ASG, Pereira MF, Blanco AJV, Franceschinelli EV. High genetic diversity and strong spatial genetic structure in Cabralea canjerana (Vell.) Mart. (Meliaceae): implications to Brazilian Atlantic Forest tree conservation. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.ncon.2014.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genetic characterization and structure of the endemic Colombian silvery brown bare-face tamarin, Saguinus leucopus (Callitrichinae, Cebidae, Primates). Primates 2014; 55:415-35. [PMID: 24817278 DOI: 10.1007/s10329-014-0418-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
We analyzed 115 Saguinus leucopus, from four Colombian departments (Antioquia, Bolivar, Caldas and Tolima ), for 701 bp of the mt COII gene and at 10 microsatellite loci to estimate gene diversity levels, possible molecular subspecies and historical demographic changes in this species. This endemic Colombian species showed an elevated gene diversity in this gene, although its geographical distribution is very restrictive and extremely threatened by habitat fragmentation. The mt COII gene did not show any geographical structure in the distribution of the haplotypes within this species, but it did show a noteworthy population expansion throughout the history of this species. A Bayesian analysis showed that the haplotype diversification of this species began around 1.6 million years ago (MYA), whilst a haplotype network gave the beginning of this diversification at around 0.5-0.6 MYA. Forty-seven individuals out of the 115 were analyzed for 10 DNA microsatellites. The genetic diversity was relatively elevated for this kind of marker too, and comparable to that found in other Neotropical monkeys with a wider geographical distribution. Two gene pools were detected with the microsatellites, one in the northern distribution area (Antioquia) and the other in the southern distribution area (Tolima). No tests detected any bottleneck affecting this population; however, two procedures (k test and Kimmel et al. 1998 test) detected significant population expansion for the microsatellite markers, like that seen with the mt COII gene.
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Fang Z, Gonzales AM, Clegg MT, Smith KP, Muehlbauer GJ, Steffenson BJ, Morrell PL. Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3 (BETHESDA, MD.) 2014; 4:1193-203. [PMID: 24760390 PMCID: PMC4455769 DOI: 10.1534/g3.114.010561] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/22/2014] [Indexed: 12/30/2022]
Abstract
Genetic differentiation in natural populations is driven by geographic distance and by ecological or physical features within and between natural habitats that reduce migration. The primary population structure in wild barley differentiates populations east and west of the Zagros Mountains. Genetic differentiation between eastern and western populations is uneven across the genome and is greatest on linkage groups 2H and 5H. Genetic markers in these two regions demonstrate the largest difference in frequency between the primary populations and have the highest informativeness for assignment to each population. Previous cytological and genetic studies suggest there are chromosomal structural rearrangements (inversions or translocations) in these genomic regions. Environmental association analyses identified an association with both temperature and precipitation variables on 2H and with precipitation variables on 5H.
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Affiliation(s)
- Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Ana M Gonzales
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Arnaud-Haond S, Moalic Y, Hernandez-Garcia E, Eguiluz VM, Alberto F, Serrao EA, Duarte CM. Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites. J Hered 2014; 105:532-541. [DOI: 10.1093/jhered/esu015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/23/2014] [Indexed: 11/13/2022] Open
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Calderón L, Quintana F, Cabanne GS, Lougheed SC, Tubaro PL. Phylogeography and genetic structure of two Patagonian shag species (Aves: Phalacrocoracidae). Mol Phylogenet Evol 2014; 72:42-53. [PMID: 24418531 DOI: 10.1016/j.ympev.2013.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/24/2013] [Accepted: 12/31/2013] [Indexed: 11/26/2022]
Abstract
We compared the phylogeographic and genetic structure of two sympatric shag species, Phalacrocorax magellanicus (rock shag) and Phalacrocorax atriceps (imperial shag), from Patagonia (southern South America). We used multilocus genotypes of nuclear DNA (microsatellite loci) from 324 individuals and mitochondrial DNA sequences (ATPase) from 177 individuals, to evaluate hypotheses related to the effect of physical and non-physical barriers on seabird evolution. Despite sharing many ecological traits, the focal species strongly differ in two key aspects: P. magellanicus has a strong tendency to remain at/near their breeding colonies during foraging trips and the non-breeding season, while P. atriceps exhibits the converse pattern. Both species showed similar mtDNA genetic structure, where colonies from the Atlantic Coast, Pacific Coast and Fuegian region were genetically divergent. We also found similarities in the results of Bayesian clustering analysis of microsatellites, with both species having four clusters. However population differentiation (e.g. Fst, Φst) was higher in P. magellanicus compared to P. atriceps, and average membership probabilities of individuals to specific clusters (Q-values) were also higher in the former. Phalacrocorax magellanicus has strong phylogeographic structure, consistent with the impact of Pleistocene glaciations, with diagnostic haplotypes associated with each of the three mentioned regions. The same pattern was not as evident for P. atriceps. Migration rate estimators were higher for P. atriceps than for P. magellanicus; however both species followed an n-island-like model of gene flow, this implies that dispersal occurs across the continental land mass that separates Atlantic and Pacific Oceans. Our results supported the hypothesis that non-physical barriers are important drivers of the genetic and phylogeographic structure in seabirds, and also that physical barriers constitute effective but not absolute impediments to gene flow.
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Affiliation(s)
- Luciano Calderón
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Av. Angel Gallardo 470, C1405DJR Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Flavio Quintana
- Biología y Manejo de Recursos Acuáticos, Centro Nacional Patagónico, CONICET, Blvd. Brown 2915, U9120ACD Puerto Madryn, Chubut, Argentina; Wildlife Conservation Society, Amenabar 1595, C1426AKC Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Gustavo S Cabanne
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Av. Angel Gallardo 470, C1405DJR Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Stephen C Lougheed
- Queen's University, Department of Biology, Kingston, Ontario K7L3N6, Canada
| | - Pablo L Tubaro
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Av. Angel Gallardo 470, C1405DJR Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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Salmenkova EA, Omelchenko VT, Rubtsova GA, Afanas’ev KI, Romanov NS, Kovalev MY. Population genetic differentiation of white-spotted char Salvelinus leucomaenis (Pallas) in Russian Far East. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795413100098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lovatt FM, Hoelzel AR. Impact on Reindeer (Rangifer tarandus) Genetic Diversity from Two Parallel Population Bottlenecks Founded from a Common Source. Evol Biol 2013. [DOI: 10.1007/s11692-013-9263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.
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Affiliation(s)
- Kyung Seok Kim
- College of Veterinary Medicine, Seoul National University, Seoul, South Korea
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Quaternary population dynamics of an endemic conifer, Picea omorika, and their conservation implications. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0523-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Population and Conservation Genetics of Crawfish Frogs,Lithobates areolatus, at Their Northeastern Range Limit. J HERPETOL 2013. [DOI: 10.1670/12-034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Genetic diversity, fixation and differentiation of the freshwater snail Biomphalaria pfeifferi (Gastropoda, Planorbidae) in arid lands. Genetica 2013; 141:171-84. [PMID: 23543205 DOI: 10.1007/s10709-013-9715-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
Abstract
The freshwater snail Biomphalaria pfeifferi is the main intermediate host of human intestinal Bilharziasis. It is widely distributed in Africa, Madagascar and middle-eastern countries, and its habitat includes wetlands, and arid to semi-arid areas. Based on analysis of 18 microsatellites, we investigated reference allelic variation among 30 populations of B. pfeifferi from three drainage basins in Dhofar, Oman (the eastern limit of its distribution). This is an arid to semi-arid region, with a 9,000-year history of very low rainfall, but is subject to unpredictable and destructive flash floods. In this context we showed that genetic fixation was very high compared to genetic differentiation which was moderate and, that, relative to B. pfeifferi populations from wetlands, the populations in Dhofar show evidence of lower levels of genetic diversity, a higher degree of genetic fixation, a quasi-absence of migration, and a higher level of genetic drift. Despite the extreme conditions in the Dhofar habitat of this species, it is able to survive because of its very high self-fertilization (approaching 100 %) and fecundity rates.
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Khanshour A, Conant E, Juras R, Cothran EG. Microsatellite Analysis of Genetic Diversity and Population Structure of Arabian Horse Populations. J Hered 2013; 104:386-98. [DOI: 10.1093/jhered/est003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lima MR, Macedo RHF, Martins TLF, Schrey AW, Martin LB, Bensch S. Genetic and morphometric divergence of an invasive bird: the introduced house sparrow (Passer domesticus) in Brazil. PLoS One 2012; 7:e53332. [PMID: 23285283 PMCID: PMC3532305 DOI: 10.1371/journal.pone.0053332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/30/2012] [Indexed: 11/24/2022] Open
Abstract
Introduced species are interesting systems for the study of contemporary evolution in new environments because of their spatial and temporal scales. For this study we had three aims: (i) to determine how genetic diversity and genetic differentiation of introduced populations of the house sparrow (Passer domesticus) in Brazil varies with range expansion, (ii) to determine how genetic diversity and differentiation in Brazil compares to ancestral European populations; and (iii) to determine whether selection or genetic drift has been more influential on phenotypic divergence. We used six microsatellite markers to genotype six populations from Brazil and four populations from Europe. We found slightly reduced levels of genetic diversity in Brazilian compared to native European populations. However, among introduced populations of Brazil, we found no association between genetic diversity and time since introduction. Moreover, overall genetic differentiation among introduced populations was low indicating that the expansion took place from large populations in which genetic drift effects would likely have been weak. We found significant phenotypic divergence among sites in Brazil. Given the absence of a spatial genetic pattern, divergent selection and not genetic drift seems to be the main force behind most of the phenotypic divergence encountered. Unravelling whether microevolution (e.g., allele frequency change), phenotypic plasticity, or both mediated phenotypic divergence is challenging and will require experimental work (e.g., common garden experiments or breeding programs).
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Affiliation(s)
- Marcos R. Lima
- Departamento de Ecologia – IB, Pós-Graduação em Ecologia, Universidade de Brasília, Brasília, Brazil
| | | | - Thaís L. F. Martins
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Tremough, Penryn, Cornwall, United Kingdom
| | - Aaron W. Schrey
- Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America
| | - Lynn B. Martin
- Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America
| | - Staffan Bensch
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
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Origin of the chromosomal radiation of Madeiran house mice: a microsatellite analysis of metacentric chromosomes. Heredity (Edinb) 2012; 110:380-8. [PMID: 23232832 DOI: 10.1038/hdy.2012.107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Chromosome races of Mus musculus domesticus are characterised by particular sets of metacentric chromosomes formed by Robertsonian fusions and whole-arm reciprocal translocations. The Atlantic island of Madeira is inhabited by six chromosome races of house mice with 6-9 pairs of metacentric chromosomes. Three of these races are characterised by the metacentric 3.8 also found elsewhere in the distribution of M. m. domesticus, including Denmark and Spain. We investigated the possibility that metacentric 3.8 was introduced to Madeira during the initial colonisation, as this could have 'seeded' the cascade of chromosomal mutation that is the basis of the extraordinary chromosomal radiation observed on the island. Variation at 24 microsatellite loci mapping to three different chromosomal regions (proximal, interstitial and distal) of mouse chromosomes 3 and 8 was investigated in 179 mice from Madeira, Denmark, Portugal, Spain, Italy and Scotland. Analyses of microsatellite loci closely linked to the centromeres of these chromosomes ('proximal loci') do not support a common evolutionary origin of metacentric 3.8 among Madeiran, Danish and Spanish mouse populations. Our results suggest that Madeiran mice are genetically more similar to standard karyotype mice from Portugal than to metacentric mice from elsewhere. There is expected to be an interruption to gene flow between hybridising metacentric races on Madeira, particularly in the chromosomal regions close to the rearrangement breakpoints. Consistent with this, relating to differentiation involving chromosomes 3 and 8 on Madeira, we found greater genetic structure among races for proximal than interstitial or distal loci.
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Allen JM, Miyamoto MM, Wu CH, E Carter T, Ungvari-Martin J, Magrini K, Chapman CA. Primate DNA suggests long-term stability of an African rainforest. Ecol Evol 2012; 2:2829-42. [PMID: 23170217 PMCID: PMC3501634 DOI: 10.1002/ece3.395] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/27/2012] [Accepted: 09/03/2012] [Indexed: 11/07/2022] Open
Abstract
Red colobus monkeys, due to their sensitivity to environmental change, are indicator species of the overall health of their tropical rainforest habitats. As a result of habitat loss and overhunting, they are among the most endangered primates in the world, with very few viable populations remaining. Traditionally, extant indicator species have been used to signify the conditions of their current habitats, but they have also been employed to track past environmental conditions by detecting previous population fluctuations. Kibale National Park (KNP) in Uganda harbors the only remaining unthreatened large population of red colobus. We used microsatellite DNA to evaluate the historical demography of these red colobus and, therefore, the long-term stability of their habitat. We find that the red colobus population throughout KNP has been stable for at least ∼40,000 years. We interpret this result as evidence of long-term forest stability because a change in the available habitat or population movement would have elicited a corresponding change in population size. We conclude that the forest of what is now Kibale National Park may have served as a Late Pleistocene refuge for many East African species.
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Affiliation(s)
- Julie M Allen
- Florida Museum of Natural History, Dickinson Hall, Museum Road and Newell Drive, University of Florida Gainesville, Florida, 32611 ; Department of Biology, University of Florida Box 118525, Gainesville, Florida, 32611-8525
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Collevatti RG, de Castro TG, de Souza Lima J, de Campos Telles MP. Phylogeography of Tibouchina papyrus (Pohl) Toledo (Melastomataceae), an endangered tree species from rocky savannas, suggests bidirectional expansion due to climate cooling in the Pleistocene. Ecol Evol 2012; 2:1024-35. [PMID: 22837846 PMCID: PMC3399167 DOI: 10.1002/ece3.236] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 02/05/2012] [Accepted: 02/08/2012] [Indexed: 11/05/2022] Open
Abstract
Many endemic species present disjunct geographical distribution; therefore, they are suitable models to test hypotheses about the ecological and evolutionary mechanisms involved in the origin of disjunct distributions in these habitats. We studied the genetic structure and phylogeography of Tibouchina papyrus (Melastomataceae), endemic to rocky savannas in Central Brazil, to test hypothesis of vicariance and dispersal in the origin of the disjunct geographical distribution. We sampled 474 individuals from the three localities where the species is reported: Serra dos Pirineus, Serra Dourada, and Serra de Natividade. Analyses were based on the polymorphisms at cpDNA and on nuclear microsatellite loci. To test for vicariance and dispersal we constructed a median-joining network and performed an analysis of molecular variance (AMOVA). We also tested population bottleneck and estimated demographic parameters and time to most recent common ancestor (TMRCA) using coalescent analyses. A remarkable differentiation among populations was found. No significant effect of population expansion was detected and coalescent analyses showed a negligible gene flow among populations and an ancient coalescence time for chloroplast genome. Our results support that the disjunct distribution of T. papyrus may represent a climatic relict. With an estimated TMRCA dated from ∼836.491 ± 107.515 kyr BP (before present), we hypothesized that the disjunct distribution may be the outcome of bidirectional expansion of the geographical distribution favored by the drier and colder conditions that prevailed in much of Brazil during the Pre-Illinoian glaciation, followed by the retraction as the climate became warmer and moister.
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Affiliation(s)
- Rosane Garcia Collevatti
- Laboratório de Genética e Biodiversidade, Departamento de Biologia Geral, ICB, Universidade Federal de Goiás CxP. 131, 74001-970 Goiânia, GO, Brazil
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43
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Limborg MT, Hanel R, Debes PV, Ring AK, André C, Tsigenopoulos CS, Bekkevold D. Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus). Heredity (Edinb) 2012; 109:96-107. [PMID: 22549515 PMCID: PMC3400746 DOI: 10.1038/hdy.2012.18] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 03/02/2012] [Accepted: 03/15/2012] [Indexed: 01/28/2023] Open
Abstract
Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.
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Affiliation(s)
- M T Limborg
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - R Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen-Institut (vTI), Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - P V Debes
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - A K Ring
- Department of Marine Ecology – Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - C André
- Department of Marine Ecology – Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - C S Tsigenopoulos
- Institute of Marine Biology and Genetics (IMBG), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - D Bekkevold
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
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Wang Y, Fu D, Xia J. The genetic diversity of the noble scallop (Chlamys nobilis, Reeve 1852) in China assessed using five microsatellite markers. Mar Genomics 2012; 9:63-7. [PMID: 23904061 DOI: 10.1016/j.margen.2012.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 05/31/2012] [Accepted: 06/06/2012] [Indexed: 11/18/2022]
Abstract
Five highly variable microsatellite loci were used to investigate the genetic diversity and population structure of the noble scallop Chlamys nobilis, in the South China Sea. A total of 200 individual scallops from 4 populations were genotyped. All of the 5 microsatellite loci screened in this study showed polymorphism. A total of 32 different alleles were observed over all loci. The number of alleles per locus ranged from 3 to 12. The average allelic number of these polymorphic markers was 6.4. The averages of observed (Ho) and expected heterozygosity (He) ranged from 0.07 to 0.32 and from 0.119 to 0.459, respectively. A highly significant deviation from the Hardy-Weinberg Law, owing primarily to heterozygote deficiency, was found in all populations studied. The Nanao population exhibited more genetic diversity than the other three populations in terms of allele richness and observed and expected heterozygosity.
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Affiliation(s)
- Yanhong Wang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, CAS, Guangdong key laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 Xingang West Road, Guangzhou, 510301, China.
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Lacau H, Gayden T, Regueiro M, Chennakrishnaiah S, Bukhari A, Underhill PA, Garcia-Bertrand RL, Herrera RJ. Afghanistan from a Y-chromosome perspective. Eur J Hum Genet 2012; 20:1063-70. [PMID: 22510847 DOI: 10.1038/ejhg.2012.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.
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Affiliation(s)
- Harlette Lacau
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande). Int J Mol Sci 2012; 13:2863-2876. [PMID: 22489130 PMCID: PMC3317692 DOI: 10.3390/ijms13032863] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 01/01/2023] Open
Abstract
The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.
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Burgos-Paz W, Cerón-Muñoz M, Solarte-Portilla C. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia. Genet Mol Biol 2012; 34:711-8. [PMID: 22215979 PMCID: PMC3229130 DOI: 10.1590/s1415-47572011005000057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 08/05/2011] [Indexed: 11/30/2022] Open
Abstract
The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.
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Affiliation(s)
- William Burgos-Paz
- Grupo de Investigación en Genética, Mejoramiento y Modelación Animal, Facultad Ciencias Agrarias, Universidad de Antioquia, Medellín, Colombia
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Amavet PS, Vilardi JC, Rueda EC, Larriera A, Saidman BO. Mating system and population analysis of the broad-snouted caiman (Caiman latirostris) using microsatellite markers. AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853812x624423] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The knowledge about reproductive strategies of a species contributes to their conservation. Multiple paternity is a reproductive behavior increasing effective population size, which could increase genetic diversity particularly in populations submitted to bottlenecks events. In Argentina, wild populations of Caiman latirostris are subject of a management plan devoted to their preservation and sustainable utilization based on its commercial interest. This program started in response to the evident numeric reduction of the populations, as a consequence of hunting pressure and habitat modification; it had a remarkable success in population recovery allowing the commercial use of C. latirostris. Data on reproductive behavior of C. latirostris are limited because mating occurs in the water and the information about their genetic diversity is scarce too. Our specific aims were to study the mating system and population genetic structure applying microsatellite markers in twelve C. latirostris families. The obtained results showed highly significant difference among populations and a lack of correspondence between geographical distance and genetic differentiation suggesting that populations of C. latirostris represent unstable metapopulations. In the paternity analysis was detected more than one father in two nests, which could be explained by capacity of storage sperm, proposed in females of a related species. The behavior of multipaternity could contribute to maintain viable populations of C. latirostris, since the maintenance of genetic variability within populations could help increase their capacity to respond to selective pressure. Further studies employing genetic and behavioral framework are needed to better understand the reproductive biology of C. latirostris.
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Affiliation(s)
- Patricia Susana Amavet
- 1Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe 3000, Argentina
- 3Proyecto Yacaré-Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC-UNL/MASPyMA), A. del Valle 8700, Santa Fe 3000, Argentina
- 4Carrera del Investigador Científico (CIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Juan César Vilardi
- 2Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires 1428, Argentina
- 4Carrera del Investigador Científico (CIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Eva Carolina Rueda
- 1Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - Alejandro Larriera
- 1Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe 3000, Argentina
- 3Proyecto Yacaré-Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC-UNL/MASPyMA), A. del Valle 8700, Santa Fe 3000, Argentina
| | - Beatriz Ofelia Saidman
- 2Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires 1428, Argentina
- 4Carrera del Investigador Científico (CIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
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Hangartner S, Laurila A, Räsänen K. Adaptive divergence in moor frog (Rana arvalis) populations along an acidification gradient: inferences from Q(st) -F(st) correlations. Evolution 2011; 66:867-881. [PMID: 22380445 DOI: 10.1111/j.1558-5646.2011.01472.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microevolutionary responses to spatial variation in the environment seem ubiquitous, but the relative role of selection and neutral processes in driving phenotypic diversification remain often unknown. The moor frog (Rana arvalis) shows strong phenotypic divergence along an acidification gradient in Sweden. We here used correlations among population pairwise estimates of quantitative trait (P(ST) or Q(ST) from common garden estimates of embryonic acid tolerance and larval life-history traits) and neutral genetic divergence (F(ST) from neutral microsatellite markers), as well as environmental differences (pond pH, predator density, and latitude), to test whether this phenotypic divergence is more likely due to divergent selection or neutral processes. We found that trait divergence was more strongly correlated with environmental differences than the neutral marker divergence, suggesting that divergent natural selection has driven phenotypic divergence along the acidification gradient. Moreover, pairwise P(ST) s of embryonic acid tolerance and Q(ST) s of metamorphic size were strongly correlated with breeding pond pH, whereas pairwise Q(ST) s of larval period and growth rate were more strongly correlated with geographic distance/latitude and predator density, respectively. We suggest that incorporating measurements of environmental variation into Q(ST) -F(ST) studies can improve our inferential power about the agents of natural selection in natural populations.
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Affiliation(s)
- Sandra Hangartner
- EAWAG, Department of Aquatic Ecology and ETH-Zurich, Institute of Integrative Biology (IBZ), Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland E-mail: and Conservation Biology/Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Anssi Laurila
- EAWAG, Department of Aquatic Ecology and ETH-Zurich, Institute of Integrative Biology (IBZ), Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland E-mail: and Conservation Biology/Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Katja Räsänen
- EAWAG, Department of Aquatic Ecology and ETH-Zurich, Institute of Integrative Biology (IBZ), Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland E-mail: and Conservation Biology/Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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50
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Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists. Eur J Hum Genet 2011; 20:313-20. [PMID: 22085901 DOI: 10.1038/ejhg.2011.192] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Armenia, situated between the Black and Caspian Seas, lies at the junction of Turkey, Iran, Georgia, Azerbaijan and former Mesopotamia. This geographic position made it a potential contact zone between Eastern and Western civilizations. In this investigation, we assess Y-chromosomal diversity in four geographically distinct populations that represent the extent of historical Armenia. We find a striking prominence of haplogroups previously implicated with the Agricultural Revolution in the Near East, including the J2a-M410-, R1b1b1(*)-L23-, G2a-P15- and J1-M267-derived lineages. Given that the Last Glacial Maximum event in the Armenian plateau occured a few millennia before the Neolithic era, we envision a scenario in which its repopulation was achieved mainly by the arrival of farmers from the Fertile Crescent temporally coincident with the initial inception of farming in Greece. However, we detect very restricted genetic affinities with Europe that suggest any later cultural diffusions from Armenia to Europe were not associated with substantial amounts of paternal gene flow, despite the presence of closely related Indo-European languages in both Armenia and Southeast Europe.
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