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Sanderson MJ, Búrquez A, Copetti D, McMahon MM, Zeng Y, Wojciechowski MF. Origin and diversification of the saguaro cactus (Carnegiea gigantea): a within-species phylogenomic analysis. Syst Biol 2022; 71:1178-1194. [PMID: 35244183 DOI: 10.1093/sysbio/syac017] [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: 03/25/2020] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects post-glacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.
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Affiliation(s)
- Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Alberto Búrquez
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721 USA
| | | | - Yichao Zeng
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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2
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Palacio-Mejía JD, Grabowski PP, Ortiz EM, Silva-Arias GA, Haque T, Des Marais DL, Bonnette J, Lowry DB, Juenger TE. Geographic patterns of genomic diversity and structure in the C 4 grass Panicum hallii across its natural distribution. AOB PLANTS 2021; 13:plab002. [PMID: 33708370 PMCID: PMC7937184 DOI: 10.1093/aobpla/plab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 06/01/2023]
Abstract
Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
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Affiliation(s)
| | - Paul P Grabowski
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Edgardo M Ortiz
- Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva-Arias
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David L Des Marais
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Díaz‐Cárdenas B, Ruiz‐Sanchez E, Gadsden H, García‐Enriquez JM, Castro‐Felix P, Castañeda‐Gaytán G, Santerre A. Physiographic and climatic events in the Chihuahuan Desert lead to the speciation and distinct demographic patterns of two sister Sceloporuslizards. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brenda Díaz‐Cárdenas
- Red de Diversidad Biológica del Occidente Mexicano Instituto de Ecología A. C., Centro Regional del Bajío Pátzcuaro México
- Departamento de Ecología Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Eduardo Ruiz‐Sanchez
- Departamento de Botánica y Zoología Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Héctor Gadsden
- Red de Diversidad Biológica del Occidente Mexicano Instituto de Ecología A. C., Centro Regional del Bajío Pátzcuaro México
| | - José Manuel García‐Enriquez
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | - Patricia Castro‐Felix
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
| | | | - Anne Santerre
- Departamento de Biología Celular y Molecular Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara Zapopan México
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Chattopadhyay B, Garg KM, Ray R, Rheindt FE. Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity. Proc Biol Sci 2019; 286:20190304. [PMID: 31530139 PMCID: PMC6784725 DOI: 10.1098/rspb.2019.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10-12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.
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Affiliation(s)
| | - Kritika M. Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, 560012 Karnataka, India
- Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), BG Road, Mokdumpur, Malda-732103 West Bengal, India
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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5
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Castellanos-Morales G, Paredes-Torres LM, Gámez N, Hernández-Rosales HS, Sánchez-de la Vega G, Barrera-Redondo J, Aguirre-Planter E, Vázquez-Lobo A, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Historical biogeography and phylogeny of Cucurbita: Insights from ancestral area reconstruction and niche evolution. Mol Phylogenet Evol 2018; 128:38-54. [DOI: 10.1016/j.ympev.2018.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/23/2022]
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6
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Gould BA, Palacio-Mejia JD, Jenkins J, Mamidi S, Barry K, Schmutz J, Juenger TE, Lowry DB. Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae). BMC Genomics 2018; 19:792. [PMID: 30384830 PMCID: PMC6211516 DOI: 10.1186/s12864-018-5179-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/17/2018] [Indexed: 11/13/2022] Open
Abstract
Background Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to be understood through population genomic studies. We used whole genome sequencing combined with association study of climate to discover the drivers of differentiation in the perennial C4 grass Panicum hallii. Results Sequencing of 89 natural accessions of P.hallii revealed complex population structure across the species range. Major population genomic separation was found between subspecies P.hallii var. hallii and var. filipes as well as between at least four major unrecognized subgroups within var. hallii. At least 139 genomic SNPs were significantly associated with temperature or precipitation across the range and these SNPs were enriched for non-synonymous substitutions. SNPs associated with temperature and aridity were more often found in or near genes than expected by chance and enriched for putative involvement in dormancy processes, seed maturation, response to hyperosmosis and salinity, abscisic acid metabolism, hormone metabolism, and drought recovery. Conclusions Both geography and climate adaptation contribute significantly to patterns of genome-wide variation in P.hallii. Population subgroups within P.hallii may represent early stages in the formation of ecotypes. Climate associated loci identified here represent promising targets for future research in this and other perennial grasses. Electronic supplementary material The online version of this article (10.1186/s12864-018-5179-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Billie A Gould
- Myriad Women's Health, South San Francisco, CA, 94080, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA. .,Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
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Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts. Mol Phylogenet Evol 2018; 126:92-104. [DOI: 10.1016/j.ympev.2018.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/08/2018] [Accepted: 03/20/2018] [Indexed: 01/26/2023]
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Licona-Vera Y, Ornelas JF, Wethington S, Bryan KB. Pleistocene range expansions promote divergence with gene flow between migratory and sedentary populations of Calothorax hummingbirds. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yuyini Licona-Vera
- Departamento de Biología Evolutiva, Instituto de Ecología, AC, Xalapa, Veracruz, Mexico
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D. Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2017; 104:757-771. [PMID: 28515078 DOI: 10.3732/ajb.1700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. METHODS Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. KEY RESULTS Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island (Z. lucayana) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. CONCLUSIONS Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations.
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Affiliation(s)
- Dayana E Salas-Leiva
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Alan W Meerow
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Michael Calonje
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Javier Francisco-Ortega
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- Kushlan Tropical Science Institute, 11935 Old Cutler Road, Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Vanessa Sánchez
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Lindy Knowles
- Bahamas National Trust, P. O. Box N-4105, Bay Street Business Centre, Bay Street, Nassau
| | - David Knowles
- The Bahamas, Bahamas National Trust, Abaco National Park, P.O. Box AB-20953, Marsh Harbour, Abaco, The Bahamas
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Angulo DF, Amarilla LD, Anton AM, Sosa V. Colonization in North American Arid Lands: The Journey of Agarito (Berberis trifoliolata) Revealed by Multilocus Molecular Data and Packrat Midden Fossil Remains. PLoS One 2017; 12:e0168933. [PMID: 28146559 PMCID: PMC5287450 DOI: 10.1371/journal.pone.0168933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
Here we conduct research to understand the evolutionary history of a shrubby species known as Agarito (Berberis trifoliolata), an endemic species to the Chihuahuan Desert. We identify genetic signatures based on plastid DNA and AFLP markers and perform niche modelling and spatial connectivity analyses as well as niche modelling based on records in packrats to elucidate whether orogenic events such as mountain range uplift in the Miocene or the contraction/expansion dynamics of vegetation in response to climate oscillations in the Pliocene/Pleistocene had an effect on evolutionary processes in Agarito. Our results of current niche modelling and palaeomodelling showed that the area currently occupied by Berberis trifoliolata is substantially larger than it was during the Last Interglacial period and the Last Glacial Maximum. Agarito was probably confined to small areas in the Northeastern and gradually expanded its distribution just after the Last Glacial Maximum when the weather in the Chihuahuan Desert and adjacent regions became progressively warmer and drier. The most contracted range was predicted for the Interglacial period. Populations remained in stable areas during the Last Glacial Maximum and expanded at the beginning of the Holocene. Most genetic variation occured in populations from the Sierra Madre Oriental. Two groups of haplotypes were identified: the Mexican Plateau populations and certain Northeastern populations. Haplogroups were spatially connected during the Last Glacial Maximum and separated during interglacial periods. The most important prediction of packrat middens palaeomodelling lies in the Mexican Plateau, a finding congruent with current and past niche modelling predictions for agarito and genetic results. Our results corroborate that these climate changes in the Pliocene/Pleistocene affected the evolutionary history of agarito. The journey of agarito in the Chihuahuan Desert has been dynamic, expanding and contracting its distribution range and currently occupying the largest area in its history.
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Affiliation(s)
- Diego F Angulo
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Leonardo D Amarilla
- Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ana M Anton
- Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Victoria Sosa
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
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Marilyn VC, Victoria S. New insights on the origin of the woody flora of the Chihuahuan Desert: The case of Lindleya. AMERICAN JOURNAL OF BOTANY 2016. [PMID: 27578626 DOI: 10.1111/jbi.13745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We reconstructed aspects of the evolutionary history of Lindleya, a shrubby element in the rose family, as a model for identifying the ancestral area of the biota of the Chihuahuan Desert and for understanding the effect that pre-Pleistocene or Pleistocene climate fluctuations had on the evolution of the plants of this desert. METHODS We conducted phylogenetic, biogeographic, and phylogeographic analyses based on one nuclear DNA and two plastid markers sequenced for 20 populations comprising 153 accessions and representing the species' entire distribution range. We carried out ecological niche modeling to forecast Lindleya's potential distribution under Current, Last Interglacial, and Last Glacial Maximum conditions. KEY RESULTS The ancestral area of Lindleya populations was probably in the central and southern parts of the Chihuahuan Desert. Levels of genetic and haplotype variation were the highest in the northernmost and southernmost areas and low levels of genetic variation in the central part. Extended Bayesian skyline plots including all populations identified a slight demographic expansion ∼1 Ma. The predicted potential distribution during the Last Glacial Maximum was very restricted. CONCLUSIONS We suggest that pre-Pleistocene changes had an influence on the divergence of Lindleya populations. We also suggest that the ancestral area for Lindleya was the Chihuahuan Desert and that the uplift of the Trans-Mexican Volcanic Belt isolated the Tehuacán Valley populations. Genetic and demographic analyses as well as and ecological niche modeling indicate that populations of Lindleya experienced genetic bottlenecks and that they have expanded since the Last Glacial Maximum.
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Affiliation(s)
- Vásquez-Cruz Marilyn
- Biología Evolutiva, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, El Haya 91070 Xalapa, Veracruz, Mexico
| | - Sosa Victoria
- Biología Evolutiva, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, El Haya 91070 Xalapa, Veracruz, Mexico
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Laport RG, Minckley RL, Ramsey J. Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex. AMERICAN JOURNAL OF BOTANY 2016; 103:1358-1374. [PMID: 27440793 DOI: 10.3732/ajb.1600105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions. METHODS We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs). KEY RESULTS Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation. CONCLUSIONS Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.
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Affiliation(s)
- Robert G Laport
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska 68588 USA
| | - Robert L Minckley
- University of Rochester, Department of Biology, River Campus, Rochester, New York 14627 USA
| | - Justin Ramsey
- Black Hills State University, School of Natural Sciences, Spearfish, South Dakota 57799 USA
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Castellanos-Morales G, Gámez N, Castillo-Gámez RA, Eguiarte LE. Peripatric speciation of an endemic species driven by Pleistocene climate change: The case of the Mexican prairie dog ( Cynomys mexicanus ). Mol Phylogenet Evol 2016; 94:171-81. [DOI: 10.1016/j.ympev.2015.08.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 02/02/2023]
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Quintero I, Keil P, Jetz W, Crawford FW. Historical Biogeography Using Species Geographical Ranges. Syst Biol 2015; 64:1059-73. [PMID: 26254671 PMCID: PMC4838013 DOI: 10.1093/sysbio/syv057] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 07/24/2015] [Indexed: 01/20/2023] Open
Abstract
Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this article, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis.
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Affiliation(s)
- Ignacio Quintero
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA;
| | - Petr Keil
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA; Center for Theoretical Study, Charles University and Academy of Sciences of the Czech Republic, Jilska 1, 11000 Praha 1, Czech Republic
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA
| | - Forrest W Crawford
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA; Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA
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Slovák M, Kučera J, Záveská E, Vd'ačný P. Dealing with discordant genetic signal caused by hybridisation, incomplete lineage sorting and paucity of primary nucleotide homologies: a case study of closely related members of the genus Picris subsection Hieracioides (Compositae). PLoS One 2014; 9:e104929. [PMID: 25192431 PMCID: PMC4156297 DOI: 10.1371/journal.pone.0104929] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/15/2014] [Indexed: 12/24/2022] Open
Abstract
We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups.
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Affiliation(s)
- Marek Slovák
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- * E-mail:
| | - Jaromír Kučera
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eliška Záveská
- Department of Botany, Charles University, Praha, Czech Republic
| | - Peter Vd'ačný
- Department of Zoology, Comenius University, Bratislava, Slovakia
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Escaping to the summits: Phylogeography and predicted range dynamics of Cerastium dinaricum, an endangered high mountain plant endemic to the western Balkan Peninsula. Mol Phylogenet Evol 2014; 78:365-74. [DOI: 10.1016/j.ympev.2014.05.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/05/2014] [Accepted: 05/08/2014] [Indexed: 11/17/2022]
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Ramsey J, Ramsey TS. Ecological studies of polyploidy in the 100 years following its discovery. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130352. [PMID: 24958925 PMCID: PMC4071525 DOI: 10.1098/rstb.2013.0352] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions-as achieved from divergence of physiological and life-history traits-but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910 s-1930 s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930 s-1950 s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940 s and 1950 s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s-1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990 s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy--regarded by most botanists as the primary mode of genome duplication--is largely unstudied in an ecological context.
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Affiliation(s)
- Justin Ramsey
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Tara S Ramsey
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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Spatio-temporal evolution of Leucophyllum pringlei and allies (Scrophulariaceae): A group endemic to North American xeric regions. Mol Phylogenet Evol 2014; 76:93-101. [DOI: 10.1016/j.ympev.2014.02.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/25/2014] [Accepted: 02/28/2014] [Indexed: 11/19/2022]
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Lira-Noriega A, Manthey JD. Relationship of genetic diversity and niche centrality: a survey and analysis. Evolution 2014; 68:1082-93. [PMID: 24372193 DOI: 10.1111/evo.12343] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 12/07/2013] [Indexed: 11/28/2022]
Abstract
The distribution of genetic diversity within and among populations in relation to species' geographic ranges is important to understanding processes of evolution, speciation, and biogeography. One hypothesis predicts that natural populations at geographic range margins will have lower genetic diversity relative to those located centrally in species' distributions owing to a link between geographic and environmental marginality; alternatively, genetic variation may be unrelated with geographic marginality via decoupling of geographic and environmental marginality. We investigate the predictivity of geographic patterns of genetic variation based on geographic and environmental marginality using published genetic diversity data for 40 species (insects, plants, birds, mammals, worms). Only about half of species showed positive relationships between geographic and environmental marginality. Three analyses (sign test, multiple linear regression, and meta-analysis of correlation effect sizes) showed a negative relationship between genetic diversity and distance to environmental niche centroid, but no consistent relationship of genetic diversity with distance to geographic range center.
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Affiliation(s)
- Andrés Lira-Noriega
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045; Department of Ecology and Evolutionary Biology, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045.
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Poncet V, Munoz F, Munzinger J, Pillon Y, Gomez C, Couderc M, Tranchant-Dubreuil C, Hamon S, de Kochko A. Phylogeography and niche modelling of the relict plantAmborella trichopoda(Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia. Mol Ecol 2013; 22:6163-78. [DOI: 10.1111/mec.12554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Valérie Poncet
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | - François Munoz
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
| | - Jérôme Munzinger
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
- IRD; UMR AMAP; Herbarium NOU 98848 Nouméa New Caledonia
| | - Yohan Pillon
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
- Tropical Conservation Biology and Environmental Science; University of Hawai'i at Hilo; 200 West Kawili St. Hilo HI 96720 USA
| | - Céline Gomez
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
| | - Marie Couderc
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | | | - Serge Hamon
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
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Yamashita T, Rhoads DD. Species delimitation and morphological divergence in the scorpion Centruroides vittatus (Say, 1821): insights from phylogeography. PLoS One 2013; 8:e68282. [PMID: 23861878 PMCID: PMC3702564 DOI: 10.1371/journal.pone.0068282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 05/28/2013] [Indexed: 11/18/2022] Open
Abstract
Scorpion systematics and taxonomy have recently shown a need for revision, partially due to insights from molecular techniques. Scorpion taxonomy has been difficult with morphological characters as disagreement exists among researchers with character choice for adequate species delimitation in taxonomic studies. Within the family Buthidae, species identification and delimitation is particularly difficult due to the morphological similarity among species and extensive intraspecific morphological diversity. The genus Centruroides in the western hemisphere is a prime example of the difficulty in untangling the taxonomic complexity within buthid scorpions. In this paper, we present phylogeographic, Ecological Niche Modeling, and morphometric analyses to further understand how population diversification may have produced morphological diversity in Centruroides vittatus (Say, 1821). We show that C. vittatus populations in the Big Bend and Trans-Pecos region of Texas, USA are phylogeographically distinct and may predate the Last Glacial Maximum (LGM). In addition, we suggest the extended isolation of Big Bend region populations may have created the C. vittatus variant once known as C. pantheriensis.
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Affiliation(s)
- Tsunemi Yamashita
- Department of Biological Sciences, Arkansas Tech University, Russellville, Arkansas, USA.
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PETTENGILL JAMESB, MOELLER DAVIDA. Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfingClarkia. Mol Ecol 2012; 21:4578-92. [DOI: 10.1111/j.1365-294x.2012.05715.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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BARRINGER BC, KULKA EA, GALLOWAY LF. Reduced inbreeding depression in peripheral relative to central populations of a monocarpic herb. J Evol Biol 2012; 25:1200-8. [DOI: 10.1111/j.1420-9101.2012.02510.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Refugia and geographic barriers of populations of the desert poppy, Hunnemannia fumariifolia (Papaveraceae). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0089-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Wilson JS, Pitts JP. Identifying Pleistocene refugia in North American cold deserts using phylogeographic analyses and ecological niche modelling. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00902.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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SLOVÁK MAREK, KUČERA JAROMÍR, TURIS PETER, ZOZOMOVÁ-LIHOVÁ JUDITA. Multiple glacial refugia and postglacial colonization routes inferred for a woodland geophyte, Cyclamen purpurascens: patterns concordant with the Pleistocene history of broadleaved and coniferous tree species. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01826.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Escobar García P, Winkler M, Flatscher R, Sonnleitner M, Krejčíková J, Suda J, Hülber K, Schneeweiss GM, Schönswetter P. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae). Mol Ecol 2012; 21:1255-70. [PMID: 22276934 PMCID: PMC3306793 DOI: 10.1111/j.1365-294x.2012.05456.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes.
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Affiliation(s)
- Pedro Escobar García
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, Austria
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Hamilton CA, Formanowicz DR, Bond JE. Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas. PLoS One 2011; 6:e26207. [PMID: 22022570 PMCID: PMC3192178 DOI: 10.1371/journal.pone.0026207] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 09/22/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal "barcoding gene". An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame. METHODS AND FINDINGS A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a "barcode gap" using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups. CONCLUSIONS The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a "species".
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Affiliation(s)
- Chris A. Hamilton
- Auburn University Museum of Natural History and Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Daniel R. Formanowicz
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jason E. Bond
- Auburn University Museum of Natural History and Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
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Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia. Mol Phylogenet Evol 2011; 59:444-57. [DOI: 10.1016/j.ympev.2011.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 02/05/2011] [Indexed: 11/23/2022]
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