101
|
Adams M, Wedderburn SD, Unmack PJ, Hammer MP, Johnson JB. Use of congeneric assessment to reveal the linked genetic histories of two threatened fishes in the Murray-Darling Basin, Australia. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:767-776. [PMID: 21676026 DOI: 10.1111/j.1523-1739.2011.01692.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The intensely regulated Murray-Darling Basin in southeastern Australia is the nation's most extensive and economically important river system, and it contains fragmented populations of numerous fish species. Among these is the Murray hardyhead (Craterocephalus fluviatilis), a species listed as endangered (International Union for Conservation of Nature Red List) in the mid-1990 s prior to its acute decline with the progression of a severe drought that began in 1997. We compared the genetic structure of Murray hardyhead with 4 congeneric species (Darling hardyhead[C. amniculus], Finke hardyhead[C. centralis], Lake Eyre hardyhead[C. eyresii], and unspecked hardyhead[C. stercusmuscarum]), selected on the basis of their taxonomic or biological similarity to Murray hardyhead, in order to affirm species boundaries and test for instances of introgressive hybridization, which may influence species ecology and conservation prospects. We used allozyme (52 loci) and mtDNA markers (1999 bp of ATPase and cytochrome b) to provide a comparative genetic assessment of 139 Murray hardyhead, which represented all extant and some recently extirpated populations, and 71 congeneric specimens from 12 populations. We confirmed that Murray hardyhead and Darling hardyhead are taxonomically distinct and identified a number of potential conservation units, defined with genetic criteria, in both species. We also found allozyme and mtDNA evidence of historic genetic exchange between these 2 allopatric species, apparently involving one population of each species at the geographic edge of the species' ranges, not in the most proximate populations sampled. Our results provide information on species boundaries and offer insight into the likely causes of high genetic diversity in certain populations, results which are already being used to guide national recovery planning and local action. Given the prevalence of incorrect taxonomies and introgression in many organismal groups, we believe these data point to the need to commence genetic investigations of any threatened species from an initially broad taxonomic focus.
Collapse
Affiliation(s)
- M Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia.
| | | | | | | | | |
Collapse
|
102
|
Liu J, Yu L, Arnold ML, Wu CH, Wu SF, Lu X, Zhang YP. Reticulate evolution: frequent introgressive hybridization among Chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci. BMC Evol Biol 2011; 11:223. [PMID: 21794180 PMCID: PMC3155923 DOI: 10.1186/1471-2148-11-223] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/28/2011] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. RESULTS Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. CONCLUSION This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.
Collapse
Affiliation(s)
- Jiang Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Michael L Arnold
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Chun-Hua Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Utah State University Department of Animal, Dairy & Veterinary Sciences Old Main Hill 4700 Center for Integrated Biosystems Rm315 Logan, UT 84322-4700, USA
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Xin Lu
- Department of Zoology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| |
Collapse
|
103
|
Chavez AS, Saltzberg CJ, Kenagy GJ. Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus). Mol Ecol 2011; 20:3350-66. [PMID: 21771139 DOI: 10.1111/j.1365-294x.2011.05184.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A hybrid zone along an environmental gradient should contain a clinal pattern of genetic and phenotypic variation. This occurs because divergent selection in the two parental habitats is typically strong enough to overcome the homogenizing effects of gene flow across the environmental transition. We studied hybridization between two parapatric tree squirrels (Tamiasciurus spp.) across a forest gradient over which the two species vary in coloration, cranial morphology and body size. We sampled 397 individuals at 29 locations across a 600-km transect to seek genetic evidence for hybridization; upon confirming hybridization, we examined levels of genetic admixture in relation to maintenance of phenotypic divergence despite potentially homogenizing gene flow. Applying population assignment analyses to microsatellite data, we found that Tamiasciurus douglasii and T. hudsonicus form two distinct genetic clusters but also hybridize, mostly within transitional forest habitat. Overall, based on this nuclear analysis, 48% of the specimens were characterized as T. douglasii, 9% as hybrids and 43% as T. hudsonicus. Hybrids appeared to be reproductively viable, as evidenced by the presence of later-generation hybrid genotypes. Observed clines in ecologically important phenotypic traits-fur coloration and cranial morphology-were sharper than the cline of putatively neutral mtDNA, which suggests that divergent selection may maintain phenotypic distinctiveness. The relatively recent divergence of these two species (probably late Pleistocene), apparent lack of prezygotic isolating mechanisms and geographic coincidence of cline centres for both genetic and phenotypic variation suggest that environmental factors play a large role in maintaining the distinctiveness of these two species across the hybrid zone.
Collapse
Affiliation(s)
- Andreas S Chavez
- Burke Museum and Department of Biology, University of Washington, Seattle, WA 98195, USA.
| | | | | |
Collapse
|
104
|
MILÁ BORJA, TOEWS DAVIDPL, SMITH THOMASB, WAYNE ROBERTK. A cryptic contact zone between divergent mitochondrial DNA lineages in southwestern North America supports past introgressive hybridization in the yellow-rumped warbler complex (Aves: Dendroica coronata). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01661.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
105
|
Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL. Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. PLoS One 2011; 6:e20642. [PMID: 21701575 PMCID: PMC3110795 DOI: 10.1371/journal.pone.0020642] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/06/2011] [Indexed: 11/18/2022] Open
Abstract
Conservation strategies for African elephants would be advanced by resolution of conflicting claims that they comprise one, two, three or four taxonomic groups, and by development of genetic markers that establish more incisively the provenance of confiscated ivory. We addressed these related issues by genotyping 555 elephants from across Africa with microsatellite markers, developing a method to identify those loci most effective at geographic assignment of elephants (or their ivory), and conducting novel analyses of continent-wide datasets of mitochondrial DNA. Results showed that nuclear genetic diversity was partitioned into two clusters, corresponding to African forest elephants (99.5% Cluster-1) and African savanna elephants (99.4% Cluster-2). Hybrid individuals were rare. In a comparison of basal forest "F" and savanna "S" mtDNA clade distributions to nuclear DNA partitions, forest elephant nuclear genotypes occurred only in populations in which S clade mtDNA was absent, suggesting that nuclear partitioning corresponds to the presence or absence of S clade mtDNA. We reanalyzed African elephant mtDNA sequences from 81 locales spanning the continent and discovered that S clade mtDNA was completely absent among elephants at all 30 sampled tropical forest locales. The distribution of savanna nuclear DNA and S clade mtDNA corresponded closely to range boundaries traditionally ascribed to the savanna elephant species based on habitat and morphology. Further, a reanalysis of nuclear genetic assignment results suggested that West African elephants do not comprise a distinct third species. Finally, we show that some DNA markers will be more useful than others for determining the geographic origins of illegal ivory. These findings resolve the apparent incongruence between mtDNA and nuclear genetic patterns that has confounded the taxonomy of African elephants, affirm the limitations of using mtDNA patterns to infer elephant systematics or population structure, and strongly support the existence of two elephant species in Africa.
Collapse
Affiliation(s)
- Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | | | - Victor A. David
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Kai Zhao
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Robert M. Stephens
- Advanced Biomedical Computing Center, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Alfred L. Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| |
Collapse
|
106
|
Heaney LR, Balete DS, Rickart EA, Alviola PA, Duya MRM, Duya MV, Veluz MJ, VandeVrede L, Steppan SJ. Chapter 1: Seven New Species and a New Subgenus of Forest Mice (Rodentia: Muridae: Apomys) from Luzon Island. ACTA ACUST UNITED AC 2011. [DOI: 10.3158/2158-5520-2.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
107
|
Hybridization, Mitochondrial DNA Phylogeography, and Prediction of the Early Stages of Reproductive Isolation: Lessons from New Zealand Cicadas (Genus Kikihia). Syst Biol 2011; 60:482-502. [DOI: 10.1093/sysbio/syr017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
|
108
|
Hausdorf B, Wilkens H, Strecker U. Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei). Mol Phylogenet Evol 2011; 60:89-97. [PMID: 21419231 DOI: 10.1016/j.ympev.2011.03.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 03/03/2011] [Accepted: 03/08/2011] [Indexed: 11/24/2022]
Abstract
Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.
Collapse
Affiliation(s)
- Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | | | | |
Collapse
|
109
|
Darling JA. Interspecific hybridization and mitochondrial introgression in invasive carcinus shore crabs. PLoS One 2011; 6:e17828. [PMID: 21423759 PMCID: PMC3056785 DOI: 10.1371/journal.pone.0017828] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 02/15/2011] [Indexed: 11/18/2022] Open
Abstract
Interspecific hybridization plays an important role in facilitating adaptive evolutionary change. More specifically, recent studies have demonstrated that hybridization may dramatically influence the establishment, spread, and impact of invasive populations. In Japan, previous genetic evidence for the presence of two non-native congeners, the European green crab Carcinus maenas and the Mediterranean green crab C. aestuarii, has raised questions regarding the possibility of hybridization between these sister species. Here I present analysis based on both nuclear microsatellites and the mitochondrial cytochrome C oxidase subunit I (COI) gene which unambiguously argues for a hybrid origin of Japanese Carcinus. Despite the presence of mitochondrial lineages derived from both C. maenas and C. aestuarii, the Japanese population is panmictic at nuclear loci and has achieved cytonuclear equilibrium throughout the sampled range in Japan. Furthermore, analysis of admixture at nuclear loci indicates dramatic introgression of the C. maenas mitochondrial genome into a predominantly C. aestuarii nuclear background. These patterns, along with inferences drawn from the observational record, argue for a hybridization event pre-dating the arrival of Carcinus in Japan. The clarification of both invasion history and evolutionary history afforded by genetic analysis provides information that may be critically important to future studies aimed at assessing risks posed by invasive Carcinus populations to Japan and the surrounding region.
Collapse
Affiliation(s)
- John A Darling
- Molecular Ecology Research Branch, National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, Ohio, United States of America.
| |
Collapse
|
110
|
de Moraes-Barros N, Silva JAB, Morgante JS. Morphology, molecular phylogeny, and taxonomic inconsistencies in the study ofBradypussloths (Pilosa: Bradypodidae). J Mammal 2011. [DOI: 10.1644/10-mamm-a-086.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
111
|
Jolly CJ, Burrell AS, Phillips-Conroy JE, Bergey C, Rogers J. Kinda baboons (Papio kindae) and grayfoot chacma baboons (P. ursinus griseipes) hybridize in the Kafue river valley, Zambia. Am J Primatol 2010; 73:291-303. [PMID: 21274900 DOI: 10.1002/ajp.20896] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 08/30/2010] [Accepted: 09/26/2010] [Indexed: 11/10/2022]
Abstract
The ranges of small kinda (Papio kindae) and much larger grayfooted chacma (P. ursinus griseipes) baboons adjoin in the Kafue National Park, Zambia. In a visual survey of baboons at 48 sites in the Kafue River drainage we found that, contrary to previous reports, groups at the species interface near the town of Ngoma are phenotypically diverse and presumably formed by multigenerational hybridization. Mitochondrial and/or Y-chromosome genetic markers from fecal samples (N=164) collected at 29 sites support this conclusion. Groups with phenotypic signs of a history of hybridization also had taxon-specific mitochondria and Y-haplotypes from both parental species. Although the distribution of mitochondrial haplotypes largely mirrored that of external phenotypes, a significant proportion of male specimens from grayfoot as well as hybrid groups carried kinda Y-chromosomes, and kinda Y-chromosomes were involved in all observed cases of mitochondrial/Y-chromosome discordance. These observations are consistent with, though they do not prove, a population history in which the range of chacmas and the hybrid zone have advanced at the expense of the kinda range. They also suggest that, unexpectedly, kinda male×chacma female matings are much more common than the reciprocal cross in the ancestry of hybrids. We suggest that distinctive male kinda behavior and the "juvenile" appearance of kinda baboons of both sexes, perhaps combined with obstetric difficulties of a small kinda female carrying the large offspring of a chacma male, may account for this bias.
Collapse
Affiliation(s)
- C J Jolly
- New York University, Anthropology, New York, New York 10003, USA.
| | | | | | | | | |
Collapse
|
112
|
Neiva J, Pearson GA, Valero M, Serrão EA. Surfing the wave on a borrowed board: range expansion and spread of introgressed organellar genomes in the seaweed Fucus ceranoides L. Mol Ecol 2010; 19:4812-22. [PMID: 20958817 DOI: 10.1111/j.1365-294x.2010.04853.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
For many taxa, introgression represents an important source of genetic variation, but the specific contexts allowing locally introgressed material to spread and largely replace native allelic lineages throughout a species range remain poorly understood. Recent demographic-genetic simulations of spatial expansions show that the stochastic surfing of alien alleles during range expansions may constitute a general mechanism leading to extensive introgression, but empirical evidence remain scarce and difficult to distinguish from selection. In this study, we report a compelling case of such a phenomenon in the estuarine alga Fucus ceranoides. We re-assessed the phylogenetic relationships among F. ceranoides and its marine congeners F. vesiculosus and F. spiralis using nuclear, mitochondrial and chloroplast sequence data, and conducted a mtDNA phylogeographic survey in F. ceranoides. Our phylogenetic analyses revealed a recent and asymmetric introgression of a single F. vesiculosus cytoplasm into F. ceranoides. The phylogeographic scope of introgression was striking, with native and introgressed mtDNA displaying disjunct distributions south and north of the English Channel. A putative Pleistocene climatic refugium was detected in NW Iberia, and the extensive and exclusive spread of the alien cytoplasm throughout Northern Europe was inferred to have occurred concurrently with the species post-glacial, northwards range expansion. This massive spread of a foreign organelle throughout the entire post-glacial recolonization range represents good empirical evidence of an alien cytoplasm surfing the wave of a range expansion and the first description of such a phenomenon in the marine realm.
Collapse
Affiliation(s)
- João Neiva
- Centro de Ciências do Mar, Centro de Investigação Marinha e Ambiental-Laboratório Associado, Universidade do Algarve, Gambelas, 8005-139 Faro, Portugal
| | | | | | | |
Collapse
|
113
|
Köhler F, Deein G. Hybridisation as potential source of incongruence in the morphological and mitochondrial diversity of a Thai freshwater gastropod (Pachychilidae, Brotia H. Adams, 1866). ZOOSYST EVOL 2010. [DOI: 10.1002/zoos.201000013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
114
|
Hird S, Reid N, Demboski J, Sullivan J. Introgression at differentially aged hybrid zones in red-tailed chipmunks. Genetica 2010; 138:869-83. [DOI: 10.1007/s10709-010-9470-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 01/25/2010] [Indexed: 11/30/2022]
|
115
|
MIROL PATRICIA, GIMÉNEZ MABELD, SEARLE JEREMYB, BIDAU CLAUDIOJ, FAULKES CHRISG. Population and species boundaries in the South American subterranean rodent Ctenomys in a dynamic environment. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01409.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
116
|
Klymus KE, Humfeld SC, Marshall VT, Cannatella D, Gerhardt HC. Molecular patterns of differentiation in canyon treefrogs (Hyla arenicolor): evidence for introgressive hybridization with the Arizona treefrog (H. wrightorum) and correlations with advertisement call differences. J Evol Biol 2010; 23:1425-35. [PMID: 20492086 DOI: 10.1111/j.1420-9101.2010.02008.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of genetic and behavioural diversity within morphologically similar species has led to the discovery of cryptic species complexes. We tested the hypothesis that US populations of the canyon treefrog (Hyla arenicolor) may consist of cryptic species by examining mate-attraction signals among three divergent clades defined by mtDNA. Using a multi-locus approach, we re-analysed phylogenetic relationships among the three clades and a closely related, but morphologically and behaviourally dissimilar species, the Arizona treefrog (H. wrightorum). We found evidence for introgression of H. wrightorum's mitochondrial genome into H. arenicolor. Additionally, the two-clade topology based on nuclear data is more congruent with patterns of call variation than the three-clade topology from the mitochondrial dataset. The magnitude of the call divergence is probably insufficient to promote isolation of the nuclear DNA-defined clades should they become sympatric, but further divergence in call properties significant in species identification could promote speciation in the future.
Collapse
Affiliation(s)
- K E Klymus
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA. mail:
| | | | | | | | | |
Collapse
|
117
|
He K, Li YJ, Brandley MC, Lin LK, Wang YX, Zhang YP, Jiang XL. A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Mol Phylogenet Evol 2010; 56:734-46. [PMID: 20363345 DOI: 10.1016/j.ympev.2010.03.039] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/24/2010] [Accepted: 03/30/2010] [Indexed: 11/16/2022]
Abstract
Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale+Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution.
Collapse
Affiliation(s)
- Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | | | | | | | | | | |
Collapse
|
118
|
SPINKS PHILLIPQ, THOMSON ROBERTC, BRADLEY SHAFFER H. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle,Emys marmoratain California. Mol Ecol 2010; 19:542-56. [DOI: 10.1111/j.1365-294x.2009.04451.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
119
|
SCASCITELLI M, WHITNEY KD, RANDELL RA, KING MATTHEW, BUERKLE CA, RIESEBERG LH. Genome scan of hybridizing sunflowers from Texas (Helianthus annuusandH. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Mol Ecol 2010; 19:521-41. [DOI: 10.1111/j.1365-294x.2009.04504.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
120
|
Muster C, Maddison WP, Uhlmann S, Berendonk TU, Vogler AP. Arctic-alpine distributions--metapopulations on a continental scale? Am Nat 2010; 173:313-26. [PMID: 19199524 DOI: 10.1086/596534] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cold-adapted species in the Northern Hemisphere frequently show arctic-alpine discontinuous ranges at high latitudes and on mountains farther south, but area connectivity through current and historical gene flow remains unclear. We used the coalescent-based program IMa (Isolation with Migration-analytic) to test for migration among disjunct European areas of arctic-alpine wolf spiders of the Pardosa saltuaria group. Mitochondrial (ND1) and nuclear (ITS1, 5.8S rDNA, ITS2) markers were analyzed simultaneously. Gene flow was unidirectional from Scandinavia to the Alps and the Carpathians, complex with respect to intermediate relict areas in central Europe, and very limited in outlying areas in the Balkans and Pyrenees. Population connectivity may have been greater during glacial events that might alternatively account for the inferred arctic-alpine links. A simulation study under various demographic histories (using a new module in the Mesquite package, which models episodic migration) showed that the empirical results are equally consistent with moderate levels of ongoing (continuous) migration or, alternatively, with strong migration bursts at the last glacial maximum but not at earlier times. Habitat connectivity was probably maximal during glacial events, illustrating the potential influence of ecology and life history on organismal responses to past climatic change.
Collapse
Affiliation(s)
- Christoph Muster
- Institute of Biology II, University of Leipzig, Leipzig, Germany.
| | | | | | | | | |
Collapse
|
121
|
Brelsford A, Irwin DE. INCIPIENT SPECIATION DESPITE LITTLE ASSORTATIVE MATING: THE YELLOW-RUMPED WARBLER HYBRID ZONE. Evolution 2009; 63:3050-60. [DOI: 10.1111/j.1558-5646.2009.00777.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
122
|
Keck BP, Near TJ. GEOGRAPHIC AND TEMPORAL ASPECTS OF MITOCHONDRIAL REPLACEMENT INNOTHONOTUSDARTERS (TELEOSTEI: PERCIDAE: ETHEOSTOMATINAE). Evolution 2009; 64:1410-28. [DOI: 10.1111/j.1558-5646.2009.00901.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
123
|
|
124
|
Abstract
Data analysis in phylogeographic investigations is typically conducted in either a qualitative manner, or alternatively via the testing of null hypotheses. The former, where inferences about population processes are derived from geographical patterns of genetic variation, may be subject to confirmation bias and prone to overinterpretation. Testing the predictions of null hypotheses is arguably less prone to bias than qualitative approaches, but only if the tested hypotheses are biologically meaningful. As it is difficult to know a priori if this is the case, there is the general need for additional methodological approaches in phylogeographic research. Here, we explore an alternative method for analysing phylogeographic data that utilizes information theory to quantify the probability of multiple hypotheses given the data. We accomplish this by augmenting the model-selection procedure implemented in ima with calculations of Akaike Information Criterion scores and model probabilities. We generate a ranking of 17 models each representing a set of historical evolutionary processes that may have contributed to the evolution of Plethodon idahoensis, and then quantify the relative strength of support for each hypothesis given the data using metrics borrowed from information theory. Our results suggest that two models have high probability given the data. Each of these models includes population divergence and estimates of ancestral theta that differ from estimates of descendent theta, inferences consistent with prior work in this system. However, the models disagree in that one includes migration as a parameter and one does not, suggesting that there are two regions of parameter space that produce model likelihoods that are similar in magnitude given our data. Results of a simulation study suggest that when data are simulated with migration, most of the optimal models include migration as a parameter, and further that when all of the shared polymorphism results from incomplete lineage sorting, most of the optimal models do not. The results could also indicate a lack of precision, which may be a product of the amount of data that we have collected. In any case, the information-theoretic metrics that we have applied to the analysis of our data are statistically rigorous, as are hypothesis-testing approaches, but move beyond the 'reject/fail to reject' dichotomy of conventional hypothesis testing in a manner that provides considerably more flexibility to researchers.
Collapse
Affiliation(s)
- Bryan C Carstens
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | | |
Collapse
|
125
|
IRWIN DARRENE, RUBTSOV ALEXANDERS, PANOV EUGENEN. Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01282.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
126
|
Hird S, Sullivan J. Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Mol Ecol 2009; 18:3097-109. [PMID: 19538343 DOI: 10.1111/j.1365-294x.2009.04196.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Hird
- Department of Biological Sciences, Box 443051, University of Idaho, Moscow, ID 83844-3051, USA
| | | |
Collapse
|
127
|
Barbanera F, Zuffi M, Guerrini M, Gentilli A, Tofanelli S, Fasola M, Dini F. Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: Evidence for introgressive hybridization and mitochondrial DNA capture. Mol Phylogenet Evol 2009; 52:103-14. [PMID: 19236928 DOI: 10.1016/j.ympev.2009.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 02/04/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
|
128
|
Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol 2009; 24:386-93. [PMID: 19409650 DOI: 10.1016/j.tree.2009.02.011] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 10/20/2022]
|
129
|
Spinks PQ, Shaffer HB. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization. Syst Biol 2009; 58:1-20. [PMID: 20525565 DOI: 10.1093/sysbio/syp005] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the mechanisms by which widely disjunct members of a clade came to occupy their current distribution is one of the fundamental challenges of biogeography. Here, we used data from 7 nuclear and 1 mitochondrial gene to examine the phylogenetic and biogeographic history of Emys, a clade of turtles that is broadly disjunct in western and eastern North America and Europe. We found strong disagreement between mitochondrial and nuclear gene trees, with mitochondrial DNA supporting the monophyly of the North American taxa (marmorata + blandingii) to the exclusion of the European orbicularis, and nuclear genes supporting the monophyly of (blandingii + orbicularis) to the exclusion of marmorata. We used fossil-calibrated molecular chronograms, in combination with supporting evidence from the fossil record and paleoclimatology, to identify a potential example of ancient hybridization and mitochondrial gene capture 12 million years ago, which explains this discrepancy. Based on the weight of evidence, we argue that the invasion of Eurasia by Emys orbicularis occurred about 16 Ma via a trans-Beringian land bridge. The case of Emys emphasizes how single-gene trees can be strongly affected by population processes, including hybridization, and that the effects of these processes can persist through long periods of evolutionary history. Given the chaotic state of the current taxonomy of these turtles, our work also emphasizes the care that should be used in implementing taxonomic changes based on 1 or a few gene trees and the importance of taking a conservative approach in renaming or splitting higher taxa based on apparent nonmonophyly.
Collapse
Affiliation(s)
- Phillip Q Spinks
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA.
| | | |
Collapse
|
130
|
Wahlberg N, Weingartner E, Warren AD, Nylin S. Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini). BMC Evol Biol 2009; 9:92. [PMID: 19422691 PMCID: PMC2688511 DOI: 10.1186/1471-2148-9-92] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 05/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known. RESULTS We investigate the species relationships and their evolutionary history over time in the genus Polygonia using DNA sequences from two mitochondrial gene regions (COI and ND1, total 1931 bp) and four nuclear gene regions (EF-1alpha, wingless, GAPDH and RpS5, total 2948 bp). We found clear, strongly supported conflict between mitochondrial and nuclear DNA sequences in estimating species relationships in the genus Polygonia. Nodes at which there was no conflict tended to have diverged at the same time when analyzed separately, while nodes at which conflict was present diverged at different times. We find that two species create most of the conflict, and attribute the conflict found in Polygonia satyrus to ancient hybridization and conflict found in Polygonia oreas to recent or ongoing hybridization. In both examples, the nuclear gene regions tended to give the phylogenetic relationships of the species supported by morphology and biology. CONCLUSION Studies inferring species-level relationships using molecular data should never be based on a single locus. Here we show that the phylogenetic hypothesis generated using mitochondrial DNA gives a very different interpretation of the evolutionary history of Polygonia species compared to that generated from nuclear DNA. We show that possible cases of hybridization in Polygonia are not limited to sister species, but may be inferred further back in time. Furthermore, we provide more evidence that Haldane's effect might not be as strong a process in preventing hybridization in butterflies as has been previously thought.
Collapse
Affiliation(s)
- Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland
| | | | - Andrew D Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, SW 34th Street and Hull Road, PO Box 112710, Gainesville, FL 32611-2710, USA
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-399, México, DF 04510 México
| | - Sören Nylin
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| |
Collapse
|
131
|
Current World Literature. Curr Opin Lipidol 2009; 20:135-42. [PMID: 19276892 DOI: 10.1097/mol.0b013e32832a7e09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
132
|
Mitochondrial evidence for the hybrid origin of the kipunji, Rungwecebus kipunji (Primates: Papionini). Mol Phylogenet Evol 2009; 51:340-8. [PMID: 19236932 DOI: 10.1016/j.ympev.2009.02.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 02/10/2009] [Accepted: 02/16/2009] [Indexed: 11/22/2022]
Abstract
Common baboons (Papio), gelada baboons (Theropithecus) and baboon-mangabeys (Lophocebus) are closely related African papionin monkeys. In 2005, the species Lophocebus kipunji was described from relict montane and submontane forests in Tanzania, based upon a single specimen and observations of living animals. Its initial assignment to Lophocebus was based on its overall morphology, but subsequent genetic studies suggesting that it was sister taxon to common baboons (Papio) led to its generic separation, as Rungwecebus. As a mangabey-like sister-taxon to Papio, Rungwecebus could be interpreted either as an arboreal derivative from a more terrestrial, baboon-like ancestor, or as a survivor of a mangabey-like common ancestor of the Lophocebus-Papio-Theropithecus clade. Here, we present a new, strongly-supported, mitochondrial DNA (mtDNA) phylogeny that includes Papio baboons from populations geographically close to the kipunji. Rather than supporting sister-taxon status, the new phylogeny not only situates the kipunji's mtDNA among Papio haplotypes, it clearly assigns it to a mitochondrial clade including geographically adjacent yellow baboons (Papio cynocephalus). This relationship suggests either that the kipunji is descended from a yellow baboon, and has converged on a mangabey-like morphology, or, much more likely, that it originated by hybridization between Papio cf.cynocephalus females and Lophocebus sp. males, about 0.65 Ma. We believe this to be the first case among mammals in which a natural occurrence of inter-generic hybridization can be shown to have resulted in a new, distinct, long-surviving taxon. More such cases can be anticipated as molecular evidence accumulates.
Collapse
|
133
|
Obolenskaya EV, Lee MY, Dokuchaev NE, Oshida T, Lee MS, Lee H, Lissovsky AA. Diversity of Palaearctic chipmunks (Tamias, Sciuridae). MAMMALIA 2009. [DOI: 10.1515/mamm.2009.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
134
|
|
135
|
Hailer F, Leonard JA. Hybridization among three native North American Canis species in a region of natural sympatry. PLoS One 2008; 3:e3333. [PMID: 18841199 PMCID: PMC2556088 DOI: 10.1371/journal.pone.0003333] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 08/12/2008] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Population densities of many species throughout the world are changing due to direct persecution as well as anthropogenic habitat modification. These changes may induce or increase the frequency of hybridization among taxa. If extensive, hybridization can threaten the genetic integrity or survival of endangered species. Three native species of the genus Canis, coyote (C. latrans), Mexican wolf (C. lupus baileyi) and red wolf (C. rufus), were historically sympatric in Texas, United States. Human impacts caused the latter two to go extinct in the wild, although they survived in captive breeding programs. Morphological data demonstrate historic reproductive isolation between all three taxa. While the red wolf population was impacted by introgressive hybridization with coyotes as it went extinct in the wild, the impact of hybridization on the Texas populations of the other species is not clear. METHODOLOGY/ PRINCIPAL FINDINGS We surveyed variation at maternally and paternally inherited genetic markers (mitochondrial control region sequence and Y chromosome microsatellites) in coyotes from Texas, Mexican wolves and red wolves from the captive breeding programs, and a reference population of coyotes from outside the historic red wolf range. Levels of variation and phylogenetic analyses suggest that hybridization has occasionally taken place between all three species, but that the impact on the coyote population is very small. CONCLUSION/SIGNIFICANCE Our results demonstrate that the factors driving introgressive hybridization in sympatric Texan Canis are multiple and complex. Hybridization is not solely determined by body size or sex, and density-dependent effects do not fully explain the observed pattern either. No evidence of hybridization was identified in the Mexican wolf captive breeding program, but introgression appears to have had a greater impact on the captive red wolves.
Collapse
Affiliation(s)
- Frank Hailer
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Center for Conservation and Evolutionary Genetics, National Zoological Park & National Museum of Natural History, Smithsonian Institution, Washington, D. C., United States of America
| | - Jennifer A. Leonard
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Center for Conservation and Evolutionary Genetics, National Zoological Park & National Museum of Natural History, Smithsonian Institution, Washington, D. C., United States of America
| |
Collapse
|