1
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Makhov IA, Gorodilova YYU, Lukhtanov VA. Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.
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Affiliation(s)
- Ilia A Makhov
- Department of Entomology, Saint Petersburg State University, Universitetskaya Embankment 7/9, 199034 Saint Petersburg, Russia
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
| | - Yelizaveta Y U Gorodilova
- Biological Faculty, Saint Petersburg State University, Botanicheskaya Street 17, Stary Peterhof, Saint Petersburg 198504, Russia
| | - Vladimir A Lukhtanov
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
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2
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Slager DL, Epperly KL, Ha RR, Rohwer S, Wood C, Van Hemert C, Klicka J. Cryptic and extensive hybridization between ancient lineages of American crows. Mol Ecol 2020; 29:956-969. [PMID: 32034818 DOI: 10.1111/mec.15377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.
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Affiliation(s)
- David L Slager
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kevin L Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Renee R Ha
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sievert Rohwer
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Chris Wood
- Burke Museum of Natural History and Culture, Seattle, WA, USA
| | | | - John Klicka
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
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3
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Rivera D, Prates I, Rodrigues MT, Carnaval AC. Effects of climate and geography on spatial patterns of genetic structure in tropical skinks. Mol Phylogenet Evol 2020; 143:106661. [DOI: 10.1016/j.ympev.2019.106661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
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4
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Kearns AM, Restani M, Szabo I, Schrøder-Nielsen A, Kim JA, Richardson HM, Marzluff JM, Fleischer RC, Johnsen A, Omland KE. Genomic evidence of speciation reversal in ravens. Nat Commun 2018; 9:906. [PMID: 29500409 PMCID: PMC5834606 DOI: 10.1038/s41467-018-03294-w] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2018] [Indexed: 01/10/2023] Open
Abstract
Many species, including humans, have emerged via complex reticulate processes involving hybridisation. Under certain circumstances, hybridisation can cause distinct lineages to collapse into a single lineage with an admixed mosaic genome. Most known cases of such 'speciation reversal' or 'lineage fusion' involve recently diverged lineages and anthropogenic perturbation. Here, we show that in western North America, Common Ravens (Corvus corax) have admixed mosaic genomes formed by the fusion of non-sister lineages ('California' and 'Holarctic') that diverged ~1.5 million years ago. Phylogenomic analyses and concordant patterns of geographic structuring in mtDNA, genome-wide SNPs and nuclear introns demonstrate long-term admixture and random interbreeding between the non-sister lineages. In contrast, our genomic data support reproductive isolation between Common Ravens and Chihuahuan Ravens (C. cryptoleucus) despite extensive geographic overlap and a sister relationship between Chihuahuan Ravens and the California lineage. These data suggest that the Common Raven genome was formed by secondary lineage fusion and most likely represents a case of ancient speciation reversal that occurred without anthropogenic causes.
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Affiliation(s)
- Anna M Kearns
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA.
| | - Marco Restani
- Department of Biological Sciences, St. Cloud State University, 720 Fourth Avenue, St. Cloud, MN, 56301-4498, USA
| | - Ildiko Szabo
- Cowan Tetrapod Collection, Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | | | - Jin Ah Kim
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Hayley M Richardson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - John M Marzluff
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA
| | - Arild Johnsen
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Kevin E Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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5
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Dai C, Hao Y, He Y, Lei F. The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone. BMC Evol Biol 2017; 17:266. [PMID: 29262786 PMCID: PMC5738821 DOI: 10.1186/s12862-017-1114-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses. RESULTS ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids. CONCLUSIONS Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.
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Affiliation(s)
- Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yong He
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
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6
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Johnsen A, Kearns AM, Omland KE, Anmarkrud JA. Sequencing of the complete mitochondrial genome of the common raven Corvus corax (Aves: Corvidae) confirms mitogenome-wide deep lineages and a paraphyletic relationship with the Chihuahuan raven C. cryptoleucus. PLoS One 2017; 12:e0187316. [PMID: 29084259 PMCID: PMC5662180 DOI: 10.1371/journal.pone.0187316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/17/2017] [Indexed: 11/21/2022] Open
Abstract
Previous studies based on single mitochondrial markers have shown that the common raven (Corvus corax) consists of two highly diverged lineages that are hypothesised to have undergone speciation reversal upon secondary contact. Furthermore, common ravens are paraphyletic with respect to the Chihuahuan raven (C. cryptoleucus) based on mitochondrial DNA (mtDNA). Here we explore the causes of mtDNA paraphyly by sequencing whole mitochondrial genomes of 12 common ravens from across the Northern Hemisphere, in addition to three Chihuahuan ravens and one closely related brown-necked raven (C. ruficollis) using a long-range PCR protocol. Our raven mitogenomes ranged between 16925–16928 bp in length. GC content varied from 43.3% to 43.8% and the 13 protein coding genes, two rRNAs and 22 tRNAs followed a standard avian mitochondrial arrangement. The overall divergence between the two common raven clades was 3% (range 0.3–5.8% in 16 regions including the protein coding genes, rRNAs and the control region). Phylogenies constructed from whole mitogenomes recovered the previously found mitochondrial sister relationship between the common raven California clade and the Chihuahuan raven (overall divergence 1.1%), which strengthens the hypothesis that mtDNA paraphyly in the common raven results from speciation reversal of previously distinct Holarctic and California lineages.
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Affiliation(s)
- Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
- * E-mail:
| | - Anna M. Kearns
- Natural History Museum, University of Oslo, Oslo, Norway
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Kevin E. Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
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7
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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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8
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Morinha F, Dávila JA, Bastos E, Cabral JA, Frías Ó, González JL, Travassos P, Carvalho D, Milá B, Blanco G. Extreme genetic structure in a social bird species despite high dispersal capacity. Mol Ecol 2017; 26:2812-2825. [PMID: 28222237 DOI: 10.1111/mec.14069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 01/01/2023]
Abstract
Social barriers have been shown to reduce gene flow and contribute to genetic structure among populations in species with high cognitive capacity and complex societies, such as cetaceans, apes and humans. In birds, high dispersal capacity is thought to prevent population divergence unless major geographical or habitat barriers induce isolation patterns by dispersal, colonization or adaptation limitation. We report that Iberian populations of the red-billed chough, a social, gregarious corvid with high dispersal capacity, show a striking degree of genetic structure composed of at least 15 distinct genetic units. Monitoring of marked individuals over 30 years revealed that long-distance movements over hundreds of kilometres are common, yet recruitment into breeding populations is infrequent and highly philopatric. Genetic differentiation is weakly related to geographical distance, and habitat types used are overall qualitatively similar among regions and regularly shared by individuals of different populations, so that genetic structure is unlikely to be due solely to isolation by distance or isolation by adaptation. Moreover, most population nuclei showed relatively high levels of genetic diversity, suggesting a limited role for genetic drift in significantly differentiating populations. We propose that social mechanisms may underlie this unprecedented level of genetic structure in birds through a pattern of isolation by social barriers not yet described, which may have driven this remarkable population divergence in the absence of geographical and environmental barriers.
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Affiliation(s)
- Francisco Morinha
- Laboratory of Applied Ecology, Centre for Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal.,Morinha Lab - Laboratory of Biodiversity and Molecular Genetics, Rua Dr. José Figueiredo, lote L-2, Lj B5, 5000-562, Vila Real, Portugal
| | - José A Dávila
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Estela Bastos
- Laboratory of Applied Ecology, Centre for Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, School of Life and Environmental Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - João A Cabral
- Laboratory of Applied Ecology, Centre for Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Óscar Frías
- National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - José L González
- National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Paulo Travassos
- Laboratory of Applied Ecology, Centre for Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Diogo Carvalho
- Laboratory of Applied Ecology, Centre for Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Borja Milá
- National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, 28006, Spain
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Pruett CL, Wan L, Li T, Spern C, Lance SL, Glenn T, Faircloth B, Winker K. Development and characterization of microsatellite loci for common raven (Corvus corax) and cross species amplification in other Corvidae. BMC Res Notes 2015; 8:655. [PMID: 26545581 PMCID: PMC4636899 DOI: 10.1186/s13104-015-1643-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/27/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND A priority for conservation is the identification of endemic populations. We developed microsatellite markers for common raven (Corvus corax), a bird species with a Holarctic distribution, to identify and assess endemic populations in Alaska. RESULTS From a total of 50 microsatellite loci, we isolated and characterized 15 loci. Eight of these loci were polymorphic and readily scoreable. Eighteen to 20 common ravens from Fairbanks, Alaska were genotyped showing the following variability: 3-8 alleles per locus, 0.25-0.80 observed heterozygosity (Ho), and 0.30-0.80 expected heterozygosity (He). All loci were in Hardy-Weinberg equilibrium and linkage equilibrium and many loci amplified and were polymorphic in related taxa. CONCLUSIONS These loci will be used to identify endemic populations of common raven and assess their genetic diversity and connectivity.
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Affiliation(s)
- Christin L Pruett
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
| | - Leping Wan
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
| | - Tianyu Li
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
| | - Cory Spern
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
| | - Stacey L Lance
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29802, USA.
| | - Travis Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.
| | - Brant Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
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10
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The influence of captive breeding management on founder representation and inbreeding in the ‘Alalā, the Hawaiian crow. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0788-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Nebel C, Gamauf A, Haring E, Segelbacher G, Villers A, Zachos FE. Mitochondrial DNA analysis reveals Holarctic homogeneity and a distinct Mediterranean lineage in the Golden eagle (Aquila chrysaetos). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12583] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carina Nebel
- Museum of Natural History Vienna; Vienna Austria
| | - Anita Gamauf
- Museum of Natural History Vienna; Vienna Austria
- Department of Integrative Zoology; University of Vienna; Vienna Austria
| | - Elisabeth Haring
- Museum of Natural History Vienna; Vienna Austria
- Department of Integrative Zoology; University of Vienna; Vienna Austria
| | | | - Alexandre Villers
- Centre d'Etudes Biologiques de Chizé; CNRS - Université de la Rochelle; UMR7372 Beauvoir sur Niort France
- Section of Ecology; Department of Biology; University of Turku; Turku Finland
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12
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Stewart JR, Jacobi RM. The long term response of birds to climate change: new results from a cold stage avifauna in northern England. PLoS One 2015; 10:e0122617. [PMID: 25992609 PMCID: PMC4439125 DOI: 10.1371/journal.pone.0122617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/23/2015] [Indexed: 11/22/2022] Open
Abstract
The early MIS 3 (55–40 Kyr BP associated with Middle Palaeolithic archaeology) bird remains from Pin Hole, Creswell Crags, Derbyshire, England are analysed in the context of the new dating of the site’s stratigraphy. The analysis is restricted to the material from the early MIS 3 level of the cave because the upper fauna is now known to include Holocene material as well as that from the Late Glacial. The results of the analysis confirm the presence of the taxa, possibly unexpected for a Late Pleistocene glacial deposit including records such as Alpine swift, demoiselle crane and long-legged buzzard with southern and/or eastern distributions today. These taxa are accompanied by more expected ones such as willow ptarmigan /red grouse and rock ptarmigan living today in northern and montane areas. Finally, there are temperate taxa normally requiring trees for nesting such as wood pigeon and grey heron. Therefore, the result of the analysis is that the avifauna of early MIS 3 in England included taxa whose ranges today do not overlap making it a non-analogue community similar to the many steppe-tundra mammalian faunas of the time. The inclusion of more temperate and woodland taxa is discussed in the light that parts of northern Europe may have acted as cryptic northern refugia for some such taxa during the last glacial. These records showing former ranges of taxa are considered in the light of modern phylogeographic studies as these often assume former ranges without considering the fossil record of those taxa. In addition to the anomalous combination of taxa during MIS 3 living in Derbyshire, the individuals of a number of the taxa are different in size and shape to members of the species today probably due to the high carrying capacity of the steppe-tundra.
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Affiliation(s)
- John R. Stewart
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset, BH12 5BB, United Kingdom
- * E-mail:
| | - Roger M. Jacobi
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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13
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Winger BM, Bates JM. The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru. Evolution 2015; 69:772-87. [DOI: 10.1111/evo.12607] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/07/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Benjamin M. Winger
- Committee on Evolutionary Biology; The University of Chicago; Culver Hall 402 Chicago Illinois 60637
- Life Sciences Section, Integrative Research Center; The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago Illinois 60605
| | - John M. Bates
- Committee on Evolutionary Biology; The University of Chicago; Culver Hall 402 Chicago Illinois 60637
- Life Sciences Section, Integrative Research Center; The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago Illinois 60605
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14
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Prates I, Rodrigues MT, Melo-Sampaio PR, Carnaval AC. Phylogenetic relationships of Amazonian anole lizards (Dactyloa): taxonomic implications, new insights about phenotypic evolution and the timing of diversification. Mol Phylogenet Evol 2014; 82 Pt A:258-68. [PMID: 25451806 DOI: 10.1016/j.ympev.2014.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/24/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
The ecology and evolution of Caribbean anoles are well described, yet little is known about mainland anole species. Lack of phylogenetic information limits our knowledge about species boundaries, morphological evolution, and the biogeography of anoles in South America. To help fill this gap, we provide an updated molecular phylogeny of the Dactyloa (Dactyloidae), with emphasis on the punctata species group. By sampling understudied Amazonian taxa, we (i) assess the phylogenetic placement of the 'odd anole', D. dissimilis; (ii) infer the relationships of the proboscis-bearing D. phyllorhina, testing the hypothesis of independent nasal appendage evolution within the anole radiation; and (iii) examine genetic and dewlap color variation in D. punctata and D. philopunctata. Combining multiple nuclear loci with a review of the fossil record, we also (iv) estimate divergence times within the pleurodont iguanian clade of lizards, including Amazonian representatives of Dactyloa and Norops (Dactyloidae) and of Polychrus (Polychrotidae). We recover the five Dactyloa clades previously referred to as the aequatorialis, heteroderma, latifrons, punctata and roquet species groups, as well as a sixth clade composed of D. dissimilis and the non-Amazonian D. neblinina and D. calimae. We find D. phyllorhina to be nested within the punctata group, suggesting independent evolution of the anole proboscis. We consistently recover D. philopunctata nested within D. punctata, and report limited genetic divergence between distinct dewlap phenotypes. The most recent common ancestor of Dactyloa, Anolis and Norops dates back to the Eocene. Most Amazonian taxa within both Dactyloa and Norops diverged in the Miocene, but some diversification events were as old as the late Eocene and late Oligocene. Amazonian Polychrus diverged in the Pliocene. Our findings have broad implications for anole biogeography, disputing recent suggestions that modern dactyloid genera were present in the Caribbean region during the Cretaceous.
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Affiliation(s)
- Ivan Prates
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Paulo Roberto Melo-Sampaio
- Programa de Pós-graduação em Ecologia e Manejo de Recursos Naturais and Laboratório de Herpetologia, Universidade Federal do Acre, Rio Branco, AC, Brazil; União Educacional do Norte, Rio Branco, AC, Brazil.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
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Jacobs DS, Babiker H, Bastian A, Kearney T, van Eeden R, Bishop JM. Phenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera). PLoS One 2013; 8:e82614. [PMID: 24312666 PMCID: PMC3849494 DOI: 10.1371/journal.pone.0082614] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022] Open
Abstract
Phenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi, in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R. d. damarensis, should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi, suggesting that biological constraints are unlikely to have influenced the convergence. Instead, the striking similarity in morphology and sensory biology are probably the result of neutral evolutionary processes, resulting in the independent evolution of similar phenotypes.
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Affiliation(s)
- David S. Jacobs
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Hassan Babiker
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna Bastian
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Teresa Kearney
- Ditsong Museum of Natural History, Pretoria, South Africa
| | - Rowen van Eeden
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Jacqueline M. Bishop
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
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Topp CM, Pruett CL, McCracken KG, Winker K. How migratory thrushes conquered northern North America: a comparative phylogeography approach. PeerJ 2013; 1:e206. [PMID: 24255819 PMCID: PMC3828608 DOI: 10.7717/peerj.206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/21/2013] [Indexed: 02/05/2023] Open
Abstract
Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson’s thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson’s thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species’ ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
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Affiliation(s)
- Carrie M Topp
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks , Fairbanks, AK , USA
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Birky CW. Species detection and identification in sexual organisms using population genetic theory and DNA sequences. PLoS One 2013; 8:e52544. [PMID: 23308113 PMCID: PMC3537722 DOI: 10.1371/journal.pone.0052544] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ ≥ 4) or the same species (K/θ<4) with probability ≥ 0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.
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Affiliation(s)
- C William Birky
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA.
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Kvie KS, Hogner S, Aarvik L, Lifjeld JT, Johnsen A. Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata). Ecol Evol 2012; 3:126-44. [PMID: 23404314 PMCID: PMC3568849 DOI: 10.1002/ece3.434] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 02/01/2023] Open
Abstract
Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.
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Affiliation(s)
- Kjersti S Kvie
- Natural History Museum, University of Oslo P.O. Box 1172, Blindern, N-0318, Oslo, Norway ; Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science P.O. Box 8146 Dep, N-0033, Oslo, Norway
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Whitacre JM, Atamas SP. Degeneracy allows for both apparent homogeneity and diversification in populations. Biosystems 2012; 110:34-42. [PMID: 22910487 PMCID: PMC3722245 DOI: 10.1016/j.biosystems.2012.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 01/23/2023]
Abstract
Trait diversity - the substrate for natural selection - is necessary for adaptation through selection, particularly in populations faced with environmental changes that diminish population fitness. In habitats that remain unchanged for many generations, stabilizing selection maximizes exploitation of resources by reducing trait diversity to a narrow optimal range. One might expect that such ostensibly homogeneous populations would have a reduced potential for heritable adaptive responses when faced with fitness-reducing environmental changes. However, field studies have documented populations that, even after long periods of evolutionary stasis, can still rapidly evolve in response to changed environmental conditions. We argue that degeneracy, the ability of diverse population elements to function similarly, can satisfy both the current need to maximize fitness and the future need for diversity. Degenerate ensembles appear functionally redundant in certain environmental contexts and functionally diverse in others. We propose that genetic variation not contributing to the observed range of phenotypes in a current population, also known as cryptic genetic variation (CGV), is a specific case of degeneracy. We argue that CGV, which gradually accumulates in static populations in stable environments, reveals hidden trait differences when environments change. By allowing CGV accumulation, static populations prepare themselves for future rapid adaptations to environmental novelty. A greater appreciation of degeneracy's role in resolving the inherent tension between current stabilizing selection and future directional selection has implications in conservation biology and may be applied in social and technological systems to maximize current performance while strengthening the potential for future changes.
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Affiliation(s)
- James M Whitacre
- CERCIA Computational Intelligence Lab, University of Birmingham, Edgbaston, Birmingham, UK.
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Kryukov A, Spiridonova L, Nakamura S, Haring E, Suzuki H. Comparative Phylogeography of Two Crow Species: Jungle Crow Corvus macrorhynchos and Carrion Crow Corvus corone. Zoolog Sci 2012; 29:484-92. [DOI: 10.2108/zsj.29.484] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Alexey Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Science, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Liudmila Spiridonova
- Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Science, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Sumio Nakamura
- Ornithological Society of Japan, Shinjuku, Tokyo 169-0075, Japan
| | - Elisabeth Haring
- Central Research Laboratories, Museum of Natural History, Burgring 7, 1010 Vienna, Austria
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan
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Jønsson KA, Fabre PH, Irestedt M. Brains, tools, innovation and biogeography in crows and ravens. BMC Evol Biol 2012; 12:72. [PMID: 22642364 PMCID: PMC3480872 DOI: 10.1186/1471-2148-12-72] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 04/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. RESULTS This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. CONCLUSIONS Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.
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Affiliation(s)
- Knud A Jønsson
- Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100, Copenhagen Ø, Denmark
| | - Pierre-Henri Fabre
- Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100, Copenhagen Ø, Denmark
| | - Martin Irestedt
- Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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Haring E, Däubl B, Pinsker W, Kryukov A, Gamauf A. Genetic divergences and intraspecific variation in corvids of the genus Corvus (Aves: Passeriformes: Corvidae) - a first survey based on museum specimens. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00664.x] [Citation(s) in RCA: 16] [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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WEBB WILLIAMC, MARZLUFF JOHNM, OMLAND KEVINE. Random interbreeding between cryptic lineages of the Common Raven: evidence for speciation in reverse. Mol Ecol 2011; 20:2390-402. [DOI: 10.1111/j.1365-294x.2011.05095.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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MOUSSEAU TONYA, SIKES DEREKS. Almost but not quite a subspecies: a case of genetic but not morphological diagnosability in Nicrophorus (Coleoptera: Silphidae). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2010.01568.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Rosell JA, Olson ME, Weeks A, De-Nova JA, Lemos RM, Camacho JP, Feria TP, Gómez-Bermejo R, Montero JC, Eguiarte LE. Diversification in species complexes: Tests of species origin and delimitation in the Bursera simaruba clade of tropical trees (Burseraceae). Mol Phylogenet Evol 2010; 57:798-811. [DOI: 10.1016/j.ympev.2010.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/04/2010] [Accepted: 08/09/2010] [Indexed: 11/25/2022]
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Robin VV, Sinha A, Ramakrishnan U. Ancient geographical gaps and paleo-climate shape the phylogeography of an endemic bird in the sky islands of southern India. PLoS One 2010; 5:e13321. [PMID: 20967202 PMCID: PMC2954160 DOI: 10.1371/journal.pone.0013321] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/13/2010] [Indexed: 11/21/2022] Open
Abstract
Background Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies. Methods and Principal Findings We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used Bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species. Conclusions and Significance Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region.
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Affiliation(s)
- V V Robin
- National Institute of Advanced Studies, Indian Institute of Science Campus, Bangalore, India.
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Liu JY, Brown CL, Yang TB. Phylogenetic relationships of mullets (Mugilidae) in China Seas based on partial sequences of two mitochondrial genes. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hull JM, Mindell DP, Talbot SL, Kay EH, Hoekstra HE, Ernest HB. Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani. BMC Evol Biol 2010; 10:224. [PMID: 20650000 PMCID: PMC2927923 DOI: 10.1186/1471-2148-10-224] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 07/22/2010] [Indexed: 11/25/2022] Open
Abstract
Background Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. Results To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. Conclusions These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.
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Affiliation(s)
- Joshua M Hull
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA.
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McKay BD, Zink RM. The causes of mitochondrial DNA gene tree paraphyly in birds. Mol Phylogenet Evol 2010; 54:647-50. [DOI: 10.1016/j.ympev.2009.08.024] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 08/21/2009] [Accepted: 08/25/2009] [Indexed: 11/24/2022]
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31
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Liu JY, Brown CL, Yang TB. Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China, inferred by analysis of the mitochondrial control region. BIOCHEM SYST ECOL 2009. [DOI: 10.1016/j.bse.2009.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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WIRTA H. Complex phylogeographical patterns, introgression and cryptic species in a lineage of Malagasy dung beetles (Coleoptera: Scarabaeidae). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01156.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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KIRCHMAN JEREMYJ. Genetic tests of rapid parallel speciation of flightless birds from an extant volant ancestor. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01160.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lacerda DR, Marini MA, Santos FR. Mitochondrial DNA corroborates the species distinctiveness of the Planalto (Thamnophilus pelzelni Hellmayr, 1924) and the Sooretama (T. ambiguus Swainson, 1825) Slaty-antshrikes (Passeriformes: Thamnophilidae). BRAZ J BIOL 2008; 67:873-82. [PMID: 18278354 DOI: 10.1590/s1519-69842007000500010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 12/01/2007] [Indexed: 11/21/2022] Open
Abstract
The Thamnophilus punctatus complex has been recently reviewed on the basis of morphological and vocal characters, and is divided in six different species. Two of the new species, although well defined on the basis of morphological differences, could not be unambiguously distinguished through their loud songs. The Planalto Slaty-antshrike (Thamnophilus pelzelni) and the Sooretama Slaty-antshrike (T. ambiguus) are most easily distinguished by subtle and localized changes in plumage colors of males and females. In the present study we used sequences of the control region, Cytochrome b, and ND2 genes, of the mitochondrial DNA (mtDNA) to evaluate the levels of molecular differentiation between these two species. The mean pairwise distance between the two species was 3.8%, while it varied from 2.7% to 4.9% for each mtDNA region. Although extensive variation was also detected among haplotypes within species, especially for T. ambiguus, we suggest that the genetic divergence found between T. ambiguus and T. pelzelni is high enough to corroborate the separate species status of these two antbird taxa.
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Affiliation(s)
- D R Lacerda
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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35
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Pavlova A, Zink RM, Drovetski SV, Rohwer S. Pleistocene evolution of closely related sand martins Riparia riparia and R. diluta. Mol Phylogenet Evol 2008; 48:61-73. [PMID: 18499482 DOI: 10.1016/j.ympev.2008.03.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 03/21/2008] [Accepted: 03/26/2008] [Indexed: 11/24/2022]
Abstract
Climatic fluctuations during the Quaternary resulted in a dynamic history of species' range shifts, fragmentations and expansions. Some of these events left traces in the genetic structures of plants and animals. Recent avian phylogeographic studies demonstrated that Holarctic birds responded idiosyncratically to Pleistocene climate fluctuations. We present phylogeographic analyses of the Holarctic collared sand martin (Riparia riparia) and the Asian pale sand martin (Riparia diluta), which were considered conspecific until recently. Mitochondrial and nuclear sequences confirm species status of the pale sand martin; the two species diverged sometime between late Pliocene and middle Pleistocene, but precise dates could not be provided without calibration of the substitution rate. Within the pale sand martin, we found two mitochondrial clades that are likely to have diverged in the Pleistocene, one from Central Siberia, and the other restricted to Mongolia. The two clades were sympatric with the collared sand martin in Buryatiya and Mongolia, respectively. The mitochondrial gene genealogy and phi(st) analysis of the collared sand martin haplotypes indicate recent, but not ongoing, gene exchange between North America and Eurasia, and restricted gene flow between western and eastern Siberia that likely resulted from historic fragmentation of the species' range during the last glacial maximum.
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Haring E, Gamauf A, Kryukov A. Phylogeographic patterns in widespread corvid birds. Mol Phylogenet Evol 2007; 45:840-62. [PMID: 17920300 DOI: 10.1016/j.ympev.2007.06.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 06/01/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
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Fleischer RC, Boarman WI, Gonzalez EG, Godinez A, Omland KE, Young S, Helgen L, Syed G, McIntosh CE. As the raven flies: using genetic data to infer the history of invasive common raven (Corvus corax) populations in the Mojave Desert. Mol Ecol 2007; 17:464-74. [PMID: 17908216 DOI: 10.1111/j.1365-294x.2007.03532.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Common raven (Corvus corax) populations in Mojave Desert regions of southern California and Nevada have increased dramatically over the past five decades. This growth has been attributed to increased human development in the region, as ravens have a commensal relationship with humans and feed extensively at landfills and on road-killed wildlife. Ravens, as a partially subsidized predator, also represent a problem for native desert wildlife, in particular threatened desert tortoises (Gopherus agassizii). However, it is unclear whether the more than 15-fold population increase is due to in situ population growth or to immigration from adjacent regions where ravens have been historically common. Ravens were sampled for genetic analysis at several local sites within five major areas: the West Mojave Desert (California), East Mojave Desert (southern Nevada), southern coastal California, northern coastal California (Bay Area), and northern Nevada (Great Basin). Analyses of mtDNA control region sequences reveal an increased frequency of raven 'Holarctic clade' haplotypes from south to north inland, with 'California clade' haplotypes nearly fixed in the California populations. There was significant structuring among regions for mtDNA, with high F(ST) values among sampling regions, especially between the Nevada and California samples. Analyses of eight microsatellite loci reveal a mostly similar pattern of regional population structure, with considerably smaller, but mostly significant, values. The greater mtDNA divergences may be due to lower female dispersal relative to males, lower N(e), or effects of high mutation rates on maximal values of F(ST). Analyses indicate recent population growth in the West Mojave Desert and a bottleneck in the northern California populations. While we cannot rule out in situ population growth as a factor, patterns of movement inferred from our data suggest that the increase in raven populations in the West Mojave Desert resulted from movements from southern California and the Central Valley. Ravens in the East Mojave Desert are more similar to ones from northern Nevada, indicating movement between those regions. If this interpretation of high gene flow into the Mojave Desert is correct, then efforts to manage raven numbers by local control may not be optimally effective.
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Affiliation(s)
- Robert C Fleischer
- Center for Conservation and Evolutionary Genetics, National Zoological Park & National Museum of Natural History, Smithsonian Institution, Washington, DC 20008, USA.
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38
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Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN. Comprehensive DNA barcode coverage of North American birds. MOLECULAR ECOLOGY NOTES 2007; 7:535-543. [PMID: 18784793 PMCID: PMC2259444 DOI: 10.1111/j.1471-8286.2007.01670.x] [Citation(s) in RCA: 346] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 11/20/2006] [Indexed: 11/30/2022]
Abstract
DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.
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Devitt TJ. Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition. Mol Ecol 2007; 15:4387-407. [PMID: 17107472 DOI: 10.1111/j.1365-294x.2006.03015.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.
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Affiliation(s)
- Thomas J Devitt
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA.
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40
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Kirchman JJ, Franklin JD. Comparative phylogeography and genetic structure of Vanuatu birds: control region variation in a rail, a dove, and a passerine. Mol Phylogenet Evol 2006; 43:14-23. [PMID: 17321760 DOI: 10.1016/j.ympev.2006.12.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 11/30/2006] [Accepted: 12/09/2006] [Indexed: 11/26/2022]
Abstract
We examined variation in mitochondrial control region (Domain I) sequences in three distantly related species of birds found on multiple islands in Vanuatu: the Buff-banded Rail Gallirallus philippensis (n=21, 433bp), the Emerald Dove Chalcophaps indica (n=21, 513bp), and the Streaked Fantail Rhipidura spilodera (n=17, 326bp). Nucleotide and haplotype diversity were similar in all three species and showed little to no geographic structure within Vanuatu. Estimates of demographic parameters, tests for excess rare alleles, and the structure of both haplotype networks and pairwise mismatch distributions support a hypothesis of recent colonization and subsequent expansion in C. indica and R. spilodera but not in G. philippensis. Phylogenetic analyses suggest that G. philippensis samples from Vanuatu are polyphyletic, and further indicate that this species has had a more complex history of colonization than do the other two species. Estimated divergence times of alleles sampled in Vanuatu suggest there may be slight differences among species in the timing of colonization of Vanuatu despite differences in flight ability and presumed dispersal ability. In all three species, current populations probably derive from colonists that arrived several million years after the islands formed. Our comparisons illustrate the potential of direct genetic analyses of to highlight historical differences among co-distributed species with similar levels of phenotypic variation.
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Affiliation(s)
- Jeremy J Kirchman
- Department of Zoology, University of Florida, Gainesville, Florida 32611, USA.
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41
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Omland KE, Baker JM, Peters JL. Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Mol Ecol 2006; 15:795-808. [PMID: 16499703 DOI: 10.1111/j.1365-294x.2005.02827.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many studies of phylogeography, speciation, and species limits restrict their focus to a narrow issue: gene tree monophyly. However, reciprocal monophyly does not provide an ideal touchstone criterion of any aspect of evolutionary divergence. There is a continuum of divergence stages as isolated populations go from initial allele frequency differences to well-differentiated species. Studying intermediate stages of divergence will increase our understanding of geographical speciation, species limits, and conservation priorities. We develop a conceptual framework and terminology for thinking about the stages of 'intermediate polyphyly'. The Holarctic clade of common ravens (Corvus corax), found throughout much of Eurasia and North America, provides a case study of these stages of intermediate divergence. We used coalescent, phylogenetic, and population genetic methods to investigate the history and current status of this Old World-New World distribution using 107 mitochondrial control region sequences. Phylogenetically, New World and Old World samples are intermixed. However, most samples are grouped into small subclades that are restricted to either the New World or the Old World, and only one haplotype is shared between the hemispheres. Analysis of moleculalr variance (amova) results reflect this low haplotype sharing between hemispheres (Phi(ST) = 0.13, P < 0.01). Isolation with Migration (im) coalescent results suggest a sustained period of divergence between the hemispheres and low levels of maternal gene flow. Although there has not been sufficient time to evolve reciprocal monophyly and some gene flow may occur, New World and Old World ravens are genetically quite distinct. We use this example to demonstrate these early stages of divergence as populations go from sharing only internal haplotypes, to sharing no haplotypes, to having population specific subclades. Studies of phylogeography, speciation and systematics will benefit from increased attention to these stages of intermediate polyphyly.
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Affiliation(s)
- Kevin E Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, 21250, USA.
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42
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Jacobs DS, Eick GN, Schoeman MC, Matthee CA. CRYPTIC SPECIES IN AN INSECTIVOROUS BAT, SCOTOPHILUS DINGANII. J Mammal 2006. [DOI: 10.1644/04-mamm-a-132r2.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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43
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Peters JL, Gretes W, Omland KE. Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Mol Ecol 2005; 14:3407-18. [PMID: 16156812 DOI: 10.1111/j.1365-294x.2005.02618.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
During the Late Pleistocene, glaciers sundered many species into multiple glacial refugia where populations diverged in allopatry. Although deeply divergent mitochondrial DNA (mtDNA) lineages often reflect the number of refugia occupied, it is unlikely that populations that split during the recent Wisconsin glaciations will have reached reciprocal monophyly. We examined mtDNA control region sequences from eastern and western populations of wood ducks (Aix sponsa) to determine whether their current, disjunct distribution is consistent with the occupancy of two glacial refugia. We used the 'isolation with migration' coalescent method (im) to simultaneously estimate effective population sizes, maternal gene flow, and time since divergence. We found 24 unique haplotypes, none of which were shared between the eastern and western populations, but we did not find diagnostic monophyletic lineages suggestive of long-term isolation in multiple glacial refugia. However, a high Phi ST (0.31) indicates that eastern and western populations are well differentiated in mtDNA, and results from im suggest that these populations have been diverging, without extensive gene flow, for 10,000 to 124,000 years. Results from im further suggest that these populations most likely split about 34,000 years ago, and this time of divergence is consistent with the occupancy of multiple glacial refugia during the Late Wisconsin glaciation. Eastern wood ducks are characterized by high genetic diversity, a large effective population size, and a recent population expansion, while western wood ducks have much less genetic diversity, a smaller population size, and have not undergone a recent population expansion.
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Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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44
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Peters JL, McCracken KG, Zhuravlev YN, Lu Y, Wilson RE, Johnson KP, Omland KE. Phylogenetics of wigeons and allies (Anatidae: Anas): the importance of sampling multiple loci and multiple individuals. Mol Phylogenet Evol 2005; 35:209-24. [PMID: 15737592 DOI: 10.1016/j.ympev.2004.12.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 12/20/2004] [Accepted: 12/23/2004] [Indexed: 11/20/2022]
Abstract
Species-level DNA phylogenies frequently suffer from two shortcomings--gene trees usually are constructed from a single locus, and often species are represented by only one individual. To evaluate the effect of these two shortcomings, we tested phylogenetic hypotheses within the wigeons and allies, a clade of Anas ducks (Anatidae) composed of five species. We sequenced two nuclear introns from the Z-chromosome-linked chromo-helicase binding protein gene (CHD1Zb and CHD1Za) and the mitochondrial DNA (mtDNA) control region for multiple individuals sampled from widespread geographic locations. We compared these phylogenies to previously published phylogenies constructed from morphology and protein coding regions of mtDNA. Relative to other nuclear introns, CHD showed remarkable phylogenetic utility. Of the 26 CHD1Zb alleles identified, only one was shared between two species, and the combined CHD datasets revealed that four of the five species were consistent with monophyly. Several species shared mtDNA haplotypes, which probably was a result of interspecific hybridization. Overall, the nuclear CHD tree and the mtDNA tree were more congruent with coding regions of mtDNA than they were with morphology.
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Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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45
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Johnson JA, Watson RT, Mindell DP. Prioritizing species conservation: does the Cape Verde kite exist? Proc Biol Sci 2005; 272:1365-71. [PMID: 16006325 PMCID: PMC1560339 DOI: 10.1098/rspb.2005.3098] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Cape Verde kite (Milvus milvus fasciicauda) is considered to be one of the rarest birds of prey in the world and at significant risk of extinction. For this reason there is great interest in both the taxonomic and the population status of this group. To help resolve its taxonomic status, we provide phylogenetic analyses based on three mitochondrial genes for a sampling of kites in the genus Milvus, including a broad geographical sampling of black kites (Milvus migrans), red kites (Milvus milvus), Cape Verde kite museum specimens collected between 1897 and 1924, and five kites trapped on the Cape Verde Islands during August 2002. We found that the historical Cape Verde kites, including the type specimen, were non-monophyletic and scattered within a larger red kite clade. The recently trapped kites from the Cape Verde Islands were all phylogenetically diagnosed as black kites. Our findings suggest that the traditional Cape Verde kite is not a distinctive evolutionary unit, and the case for species status, as recently suggested by others, is not supported. We do find support for recognition of at least one clade of yellow-billed kites, traditionally considered as a black kite subspecies, as a distinctive phylogenetic species.
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Affiliation(s)
- Jeff A Johnson
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA.
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46
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Abstract
European mammals have been the focus of particularly detailed taxonomic studies by traditional morphological methods. However, DNA analyses have the potential to reveal additional, cryptic species. We describe two highly divergent evolutionary lineages within a small Eurasian mammal, the field vole (Microtus agrestis). We show that the two lineages can be detected not only with maternally (mitochondrial DNA), but also with paternally (Y chromosome) and biparentally (X chromosome) inherited DNA sequences. Reciprocal monophyly of all genealogies and their congruent geographical distributions is consistent with reproductive isolation. Our results suggest that the field vole should be reclassified as two separate species.
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Affiliation(s)
- Linda Hellborg
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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47
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Adams RP, Morris JA, Pandey RN, Schwarzbach AE. Cryptic speciation between Juniperus deltoides and Juniperus oxycedrus (Cupressaceae) in the Mediterranean. BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2005.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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48
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Tonnis B, Grant PR, Grant BR, Petren K. Habitat selection and ecological speciation in Galápagos warbler finches (Certhidea olivacea and Certhidea fusca). Proc Biol Sci 2005; 272:819-26. [PMID: 15940826 PMCID: PMC1599867 DOI: 10.1098/rspb.2004.3030] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated phylogeographic divergence among populations of Galápagos warble finches. Their broad distribution, lack of phenotypic differentiation and low levels of genetic divergence make warbler finches an appropriate model to study speciation in allopatry. A positive relationship between genetic and geographical distance is expected for island taxa. Warbler finches actually showed a negative isolation by distance relationship, causing us to reject the hypothesis of distance-limited dispersal. An alternative hypothesis, that dispersal is limited by habitat similarity, was supported. We found a positive correlation between genetic distances and differences in maximum elevation among islands, which is an indicator of ecological similarity. MtDNA sequence variation revealed monophyletic support for two distinct species. Certhidea olivacea have recently dispersed among larger central islands, while some Certhidea fusca have recently dispersed to small islands at opposite ends of the archipelago. We conclude that females have chosen to breed on islands with habitats similar to their natal environment. Habitat selection is implicated as an important component of speciation of warbler finches, which is the earliest known divergence of the adaptive radiation of Darwin's finches. These results suggest that small populations can harbour cryptic but biologically meaningful variation that may affect longer term evolutionary processes.
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Affiliation(s)
- Brandon Tonnis
- Department of Biological Sciences, University of CincinnatiCincinnati, OH 45221-0006, USA
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, NJ 08544-0003, USA
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, NJ 08544-0003, USA
| | - Kenneth Petren
- Department of Biological Sciences, University of CincinnatiCincinnati, OH 45221-0006, USA
- Author for correspondence ()
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Sol D, Lefebvre L, Rodríguez-Teijeiro JD. Brain size, innovative propensity and migratory behaviour in temperate Palaearctic birds. Proc Biol Sci 2005; 272:1433-41. [PMID: 16011917 PMCID: PMC1559823 DOI: 10.1098/rspb.2005.3099] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Accepted: 03/18/2005] [Indexed: 11/12/2022] Open
Abstract
The evolution of migration in birds remains an outstanding, unresolved question in evolutionary ecology. A particularly intriguing question is why individuals in some species have been selected to migrate, whereas in other species they have been selected to be sedentary. In this paper, we suggest that this diverging selection might partially result from differences among species in the behavioural flexibility of their responses to seasonal changes in the environment. This hypothesis is supported in a comparative analysis of Palaearctic passerines. First, resident species tend to rely more on innovative feeding behaviours in winter, when food is harder to find, than in other seasons. Second, species with larger brains, relative to their body size, and a higher propensity for innovative behaviours tend to be resident, while less flexible species tend to be migratory. Residence also appears to be less likely in species that occur in more northerly regions, exploit temporally available food sources, inhabit non-buffered habitats and have smaller bodies. Yet, the role of behavioural flexibility as a response to seasonal environments is largely independent of these other factors. Therefore, species with greater foraging flexibility seem to be able to cope with seasonal environments better, while less flexible species are forced to become migratory.
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Affiliation(s)
- Daniel Sol
- Department of Biology, McGill University, 1205, Avenue Docteur Penfield, Montréal, Québec H3A 1B1 Canada.
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50
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Feldman CR, Omland KE. Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the beta-fibrinogen gene in avian molecular systematics. ZOOL SCR 2005. [DOI: 10.1111/j.1463-6409.2005.00182.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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