1
|
Yermagambetova M, Almerekova S, Ivashchenko A, Turuspekov Y, Abugalieva S. Genetic Diversity of Tulipa alberti and T. greigii Populations from Kazakhstan Based on Application of Expressed Sequence Tag Simple Sequence Repeat Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:2667. [PMID: 39339642 PMCID: PMC11435150 DOI: 10.3390/plants13182667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa greigii Regel, which are critical for biodiversity yet face significant threats from human activities. This study aimed to assess these two species' genetic diversity and population structure using 15 expressed sequence tag simple sequence repeat (EST-SSR) markers. Leaf samples from 423 individuals across 23 natural populations, including 11 populations of T. alberti and 12 populations of T. greigii, were collected and genetically characterized using EST-SSR markers. The results revealed relatively high levels of genetic variation in T. greigii compared to T. alberti. The average number of alleles per locus was 1.9 for T. alberti and 2.8 for T. greigii. AMOVA indicated substantial genetic variation within populations (75% for T. alberti and 77% for T. greigii). The Bayesian analysis of the population structure of the two species indicated an optimal value of K = 3 for both species, splitting all sampled populations into three distinct genetic clusters. Populations with the highest level of genetic diversity were identified in both species. The results underscore the importance of conserving the genetic diversity of Tulipa populations, which can help develop strategies for their preservation in stressed ecological conditions.
Collapse
Affiliation(s)
- Moldir Yermagambetova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (M.Y.); (S.A.); (Y.T.)
| | - Shyryn Almerekova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (M.Y.); (S.A.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | | | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (M.Y.); (S.A.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (M.Y.); (S.A.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| |
Collapse
|
2
|
Somoano A, Bastos-Silveira C, Ventura J, Miñarro M, Heckel G. A Bocage Landscape Restricts the Gene Flow of Pest Vole Populations. Life (Basel) 2022; 12:800. [PMID: 35743831 PMCID: PMC9225191 DOI: 10.3390/life12060800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The population dynamics of most animal species inhabiting agro-ecosystems may be determined by landscape characteristics, with agricultural intensification and the reduction of natural habitats influencing dispersal and hence limiting gene flow. Increasing landscape complexity would thus benefit many endangered species by providing different ecological niches, but it could also lead to undesired effects in species that can act as crop pests and disease reservoirs. We tested the hypothesis that a highly variegated landscape influences patterns of genetic structure in agricultural pest voles. Ten populations of fossorial water vole, Arvicola scherman, located in a bocage landscape in Atlantic NW Spain were studied using DNA microsatellite markers and a graph-based model. The results showed a strong isolation-by-distance pattern with a significant genetic correlation at smaller geographic scales, while genetic differentiation at larger geographic scales indicated a hierarchical pattern of up to eight genetic clusters. A metapopulation-type structure was observed, immersed in a landscape with a low proportion of suitable habitats. Matrix scale rather than matrix heterogeneity per se may have an important effect upon gene flow, acting as a demographic sink. The identification of sub-populations, considered to be independent management units, allows the establishment of feasible population control efforts in this area. These insights support the use of agro-ecological tools aimed at recreating enclosed field systems when planning integrated managements for controlling patch-dependent species such as grassland voles.
Collapse
Affiliation(s)
- Aitor Somoano
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Asturias, Spain;
| | - Cristiane Bastos-Silveira
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1600-214 Lisboa, Portugal;
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Natural Sciences Museum of Granollers, 08402 Barcelona, Spain
| | - Marcos Miñarro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Asturias, Spain;
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| |
Collapse
|
3
|
Molecular and Chemical Markers to Illustrate the Complex Diversity of the Genus Lupinus (Fabaceae). DIVERSITY 2021. [DOI: 10.3390/d13060263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The potential of secondary metabolites as systematic markers to get new insights in an intricate phylogeny of a recent evolutionary radiation is explored. A chemosystematic study of the genus Lupinus (Fabaceae) was performed, using quinolizidine (QA) and piperidine alkaloids (ammodendrine) as diagnostic characters. Seven major QA and the piperidine alkaloid ammodendrine were found to be the most frequent compounds. Two groups were supported according to their geographic origin: an Old World/Atlantic American group and a West New World group and this pattern is concordant with molecular data (here, based on an original barcode approach using the nuclear marker ITS). However, QA profiles are less informative at the species level. Despite a lack of resolution within the two groups, the alkaloid profiles agree with well supported clades based on DNA molecular characters. The combined use of chemical and barcode genetic markers represents a viable alternative for separating recent evolutionary lineages to a first approximation without having to resort to an expensive and sophisticated molecular arsenal such as next generation sequencing.
Collapse
|
4
|
Malenfant RM, Davis CS, Cullingham CI, Coltman DW. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis. PLoS One 2016; 11:e0148967. [PMID: 26974333 PMCID: PMC4790856 DOI: 10.1371/journal.pone.0148967] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/21/2016] [Indexed: 12/26/2022] Open
Abstract
Recently, an extensive study of 2,748 polar bears (Ursus maritimus) from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1) highly unbalanced sample sizes and large amounts of systematically missing data; (2) incorrect calculation of FST and of significance levels; (3) misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.
Collapse
Affiliation(s)
- René M. Malenfant
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
5
|
Bai WN, Wang WT, Zhang DY. Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia. THE NEW PHYTOLOGIST 2016; 209:1757-72. [PMID: 26499508 DOI: 10.1111/nph.13711] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 05/16/2023]
Abstract
East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single-copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate-induced vicariance of an ancestral northern range during the mid-Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north-south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
Collapse
Affiliation(s)
- Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wen-Ting Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- School of Mathematics and Computer Science, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
6
|
Shennan SJ, Crema ER, Kerig T. Isolation-by-distance, homophily, and “core” vs. “package” cultural evolution models in Neolithic Europe. EVOL HUM BEHAV 2015. [DOI: 10.1016/j.evolhumbehav.2014.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beheregaray LB. Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems. PLoS One 2013; 8:e82953. [PMID: 24349405 PMCID: PMC3862729 DOI: 10.1371/journal.pone.0082953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022] Open
Abstract
Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.
Collapse
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Peter J. Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Michael P. Hammer
- School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
- Curator of Fishes, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Mark Adams
- School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
- * E-mail:
| |
Collapse
|
8
|
Toit ND, van Vuuren BJ, Matthee S, Matthee CA. Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts. Mol Ecol 2013; 22:5185-204. [DOI: 10.1111/mec.12459] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/12/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Nina du Toit
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Bettine J. van Vuuren
- Centre for Invasion Biology; Department of Zoology; University of Johannesburg; PO Box 524 Auckland Park South Africa
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Conrad A. Matthee
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| |
Collapse
|
9
|
Banaticla-Hilario MCN, van den Berg RG, Hamilton NRS, McNally KL. Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 2013; 3:3047-62. [PMID: 24101993 PMCID: PMC3790550 DOI: 10.1002/ece3.689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/17/2013] [Accepted: 06/23/2013] [Indexed: 11/11/2022] Open
Abstract
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
Collapse
Affiliation(s)
- Maria Celeste N Banaticla-Hilario
- T.T. Chang Genetic Resources Center, International Rice Research Institute Los Baños, Laguna, Philippines ; Biosystematics Group, Wageningen University and Research Center Wageningen, The Netherlands
| | | | | | | |
Collapse
|
10
|
Abstract
The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non-spatial Island model.
Collapse
Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090GE Amsterdam, The Netherlands.
| |
Collapse
|
11
|
Milla R, Escudero A, Iriondo JM. Congruence between geographic range distribution and local competitive ability of two Lupinus species. AMERICAN JOURNAL OF BOTANY 2011; 98:1456-1464. [PMID: 21875973 DOI: 10.3732/ajb.1000519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY In spite of its relevance, we lack rigorous evidence on whether widespread species are superior local competitors compared with coexisting narrowly distributed congeners. We ran a competition experiment between two lupins that coexist at their shared geographic range: Lupinus angustifolius L. (widespread) and L. gredensis Gandoger (narrow endemic). • METHODS We set up mixed and monospecific populations of the two species, monitored survival and fecundity until the death of the whole cohorts, and measured variables of putative relevance to the competition process. We used aster modeling to address lifetime individual fitness and generalized linear models to assess the effect of species, type of competition, and competition environment on a suite of competition indices. • KEY RESULTS Lupinus angustifolius showed higher fitness and exerted a stronger competitive effect on its heterospecific neighbors. This occurred through higher fecundity late in the season rather than through differential survival at earlier stages. • CONCLUSIONS This is the first evidence of lifetime superior competitive potential of a widespread species over a narrow endemic congener. This competitive response might scale up to the geographic distribution range and may partially explain the limited distribution of the narrow endemic. Extension to other carefully selected study cases and more in-depth field experiments may help to assess the generality of this pattern and understand how local processes translate into geographic patterns.
Collapse
Affiliation(s)
- Rubén Milla
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/ Tulipán s/n., E-28933 Móstoles, Madrid, Spain.
| | | | | |
Collapse
|
12
|
Gomez-Uchida D, Seeb JE, Smith MJ, Habicht C, Quinn TP, Seeb LW. Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations. BMC Evol Biol 2011; 11:48. [PMID: 21332997 PMCID: PMC3049142 DOI: 10.1186/1471-2148-11-48] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 02/18/2011] [Indexed: 01/17/2023] Open
Abstract
Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.
Collapse
|
13
|
Cavallari MM, Gimenes MA, Billot C, Torres RB, Zucchi MI, Cavalheiro AJ, Bouvet JM. Population genetic relationships between Casearia sylvestris (Salicaceae) varieties occurring sympatrically and allopatrically in different ecosystems in south-east Brazil. ANNALS OF BOTANY 2010; 106:627-36. [PMID: 20699231 PMCID: PMC2944974 DOI: 10.1093/aob/mcq151] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 11/03/2009] [Accepted: 06/18/2010] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Species delimitation can be problematic, and recently diverged taxa are sometimes viewed as the extremes of a species' continuum in response to environmental conditions. Using population genetic approaches, this study assessed the relationship between two Casearia sylvestris (Salicaceae) varieties, which occur sympatrically and allopatrically in the landscape of south-east Brazil, where intermediate types are also found. METHODS In total, 376 individuals from nine populations in four different ecosystems were sampled, and nine microsatellite markers were used to assess the relative effects of the ecosystems and varieties on the distribution of genetic diversity among populations of this species. KEY RESULTS As a by-product of this study, several PCR products with more than two alleles were observed. The possibility that extra bands represent non-specific amplification or PCR artefacts was discarded by sequencing a sample of these bands. We suggest that (partial) genome duplication in C. sylvestris most probably explains this phenomenon, which may be a key factor in the differentiation of the two taxa, as it was markedly more frequent in one of the varieties. AMOVA indicated that approx. 22 % of the total genetic diversity was found between the two varieties. Bayesian analysis identified varieties and ecosystems as evolutionary units, rather than the individual populations sampled. CONCLUSIONS The results are in agreement with field observations and support the recognition of two varieties, as well as documenting the occurrence of hybridization between them.
Collapse
Affiliation(s)
- Marcelo Mattos Cavallari
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Distrito de Rubião Junior s/n, Botucatu, SP, Brazil.
| | | | | | | | | | | | | |
Collapse
|
14
|
Noble DWA, Qi Y, Fu J. Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus). BMC Evol Biol 2010; 10:197. [PMID: 20579368 PMCID: PMC2904330 DOI: 10.1186/1471-2148-10-197] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 06/25/2010] [Indexed: 11/11/2022] Open
Abstract
Background Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results. Results Assignment tests revealed two distinct nuclear DNA clusters with 95% (230/243) of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia. Conclusions These results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools for distinguishing closely related species and support the validity of P. putjatia. Assignment tests have the potential to play a significant role in elucidating biodiversity in the era of DNA data. Nonetheless, important limitations do exist and multiple independent datasets should be used to corroborate results from assignment programs.
Collapse
Affiliation(s)
- Daniel W A Noble
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | |
Collapse
|
15
|
Qiu YX, Guan BC, Fu CX, Comes HP. Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Mol Phylogenet Evol 2009; 51:281-93. [DOI: 10.1016/j.ympev.2009.01.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
16
|
Yan J, Chu HJ, Wang HC, Li JQ, Sang T. Population genetic structure of two Medicago species shaped by distinct life form, mating system and seed dispersal. ANNALS OF BOTANY 2009; 103:825-34. [PMID: 19174379 PMCID: PMC2707894 DOI: 10.1093/aob/mcp006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Life form, mating system and seed dispersal are important adaptive traits of plants. In the first effort to characterize in detail the population genetic structure and dynamics of wild Medicago species in China, a population genetic study of two closely related Medicago species, M. lupulina and M. ruthenica, that are distinct in these traits, are reported. These species are valuable germplasm resources for the improvement of Medicago forage crops but are under threat of habitat destruction. METHODS Three hundred and twenty-eight individuals from 16 populations of the annual species, M. lupulina, and 447 individuals from 15 populations of the perennial species, M. ruthenica, were studied using 15 and 17 microsatellite loci, respectively. Conventional and Bayesian-clustering analyses were utilized to estimate population genetic structure, mating system and gene flow. KEY RESULTS Genetic diversity of M. lupulina (mean H(E)=0.246) was lower than that of M. ruthenica (mean H(E)=0.677). Populations of M. lupulina were more highly differentiated (F(ST)=0.535) than those of M. ruthenica (F(ST)=0.130). For M. lupulina, 55.5% of the genetic variation was partitioned among populations, whereas 76.6% of the variation existed within populations of M. ruthenica. Based on the genetic data, the selfing rates of M. lupulina and M. ruthenica were estimated at 95.8% and 29.5%, respectively. The genetic differentiation among populations of both species was positively correlated with geographical distance. CONCLUSIONS The mating system differentiation estimated from the genetic data is consistent with floral morphology and observed pollinator visitation. There was a much higher historical gene flow in M. ruthenica than in M. lupulina, despite more effective seed dispersal mechanisms in M. lupulina. The population genetic structure and geographical distribution of the two Medicago species have been shaped by life form, mating systems and seed dispersal mechanisms.
Collapse
Affiliation(s)
- Juan Yan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- The Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Jia Chu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- The Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng-Chang Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Jian-Qiang Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- For correspondence. E-mail
| | - Tao Sang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
17
|
Drummond CS. Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats. Mol Phylogenet Evol 2008; 48:408-21. [PMID: 18534869 DOI: 10.1016/j.ympev.2008.03.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 10/22/2022]
Abstract
Previous phylogenetic studies of Lupinus (Leguminosae) based on nuclear DNA have shown that the western New World taxa form a monophyletic group representing the majority of species in the genus, with evidence for high rates of recent diversification in South America following final uplift of the Andes 2-4 million years ago (Mya). For this study, three regions of rapidly evolving non-coding chloroplast DNA (trnL intron, trnS-trnG, and trnT-trnL) were examined to estimate the timing and rates of diversification in the western New World, and to infer ancestral states for geographic range, life history, and maximum elevation. The western New World species (5.0-9.3Mya, 0.6-1.1 spp./My) comprise a basally branching assemblage of annual plants endemic to the lower elevations of western North America, from which two species-rich clades are recently derived: (i) the western North American perennials from the Rocky Mountains, Great Basin, and Pacific Slope (0.7-2.1Mya, 2.0-5.9 spp./My) and (ii) the predominantly perennial species from the Andes Mountains of South America and highlands of Mexico (0.8-3.4Mya, 1.4-5.7spp./My). Bayesian posterior predictive tests for association between life history and maximum elevation demonstrate that perennials are positively correlated with higher elevations. These results are consistent with a series of one or more recent radiations in the western New World, and indicate that rapid diversification of Lupinus coincides with the derived evolution of perennial life history, colonization of montane habitats, and range expansion from North America to South America.
Collapse
Affiliation(s)
- Christopher S Drummond
- Department of Biology, Georgetown University, 406 Reiss Sciences Building, 37th and O Streets, NW, Washington, DC 20057, USA.
| |
Collapse
|
18
|
|
19
|
Abstract
Phylogeographic studies designed to estimate rates and patterns of genetic differentiation within species often reveal unexpected and graphically striking cases of allele or haplotype sharing between species (introgression) via hybridization and backcrossing. Does introgression between species significantly influence population genetic structure relative to more conventional sources of differentiation (drift) and similarity (dispersal) among populations within species? Here we use mtDNA sequences from four species in two genera of sea urchins and sea stars to quantify the relative magnitude of gene flow across oceans and across species boundaries in the context of the trans-Arctic interchange of marine organisms between the Pacific and Atlantic oceans. In spite of the much smaller distances between sympatric congeners, rates of gene flow between sympatric species via heterospecific gamete interactions were small and significantly lower than gene flow across oceans via dispersal of planktonic larvae. We conclude that, in these cases at least, larvae are more effective than gametes as vectors of gene flow.
Collapse
Affiliation(s)
- Fiona M Harper
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
| | | | | |
Collapse
|