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Herrera ND, Bell KC, Callahan CM, Nordquist E, Sarver BAJ, Sullivan J, Demboski JR, Good JM. Genomic resolution of cryptic species diversity in chipmunks. Evolution 2022; 76:2004-2019. [PMID: 35778920 DOI: 10.1111/evo.14546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Discovery of cryptic species is essential to understand the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (Tamias amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
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Affiliation(s)
- Nathanael D Herrera
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Erin Nordquist
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brice A J Sarver
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, USA
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, University of Montana, Missoula, Montana, USA
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2
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Withnell CB, Bell CJ, Jass CN. EXTRAORDINARY ACCUMULATION OF ARVICOLINE RODENTS FROM LITTLE DELL DAM (PLEISTOCENE), UTAH. SOUTHWEST NAT 2022. [DOI: 10.1894/0038-4909-66.2.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Charles B. Withnell
- Department of Pathology and Anatomical Sciences, Kansas City University, Joplin, MO 64804 (CBW)
| | - Christopher J. Bell
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX 78712 (CJB)
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Hope AG, Frey JK. Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus). FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2021.793277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We provide a response to a recently published evaluation of the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus). The work we discuss used exon capture genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies, with recommendation that it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of this study, and explain in clearer terms how to interpret genomic analyses for applied management. We identify four broad conceptual issues that led to errant recommendations: (1) interpretation of subspecies and diagnosability, (2) inappropriate use of reciprocal monophyly as a criterion for subspecies, (3) importance of geographic isolation, and (4) error in hypothesis testing and misinterpretation of results. We conclude that the data from this genomic appraisal add to information from prior studies providing strong support for recognition of N. m. atristriatus as a subspecies. Our conclusions have important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.
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4
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Nagorsen DW, Panter N, Copley D. Phenotypes and Distribution of Yellow-Pine Chipmunk (Neotamias amoenus) of Hybrid Ancestry from the Rocky Mountains of Canada. WEST N AM NATURALIST 2021. [DOI: 10.3398/064.081.0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- David W. Nagorsen
- Royal British Columbia Museum, 675 Bellville Street, Victoria, BC V8W 9W2, Canada
| | - Nick Panter
- Royal British Columbia Museum, 675 Bellville Street, Victoria, BC V8W 9W2, Canada
| | - Darren Copley
- Royal British Columbia Museum, 675 Bellville Street, Victoria, BC V8W 9W2, Canada
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5
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Sinitsa MV, Čermák S, Kryuchkova LY. Cranial Anatomy of Csakvaromys bredai (Rodentia, Sciuridae, Xerinae) and Implications for Ground Squirrel Evolution and Systematics. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09561-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Nerva L, Iannucci A, Menchetti M, Andreoni A, Chitarra W, Martini M, Mueller N, Peeters TMJ, Pesenti E, Verbeylen G, Zozzoli R, Mori E. Where do Chip and Dale come from? Origins of invasive populations of the Siberian chipmunk in Europe. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00569-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol 2021; 70:908-921. [PMID: 33410870 DOI: 10.1093/sysbio/syaa085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.
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Affiliation(s)
- Brice A J Sarver
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| | | | - David Sneddon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho.,UC-Davis Genome Center, Davis, California
| | | | | | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana.,Wildlife Biology Program, University of Montana, Missoula, Montana
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
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Bell KC, Allen JM, Johnson KP, Demboski JR, Cook JA. Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks. Mol Phylogenet Evol 2020; 155:106998. [PMID: 33130299 DOI: 10.1016/j.ympev.2020.106998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 11/29/2022]
Abstract
The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition, the louse Hoplopleura erratica (parasitizing the eastern Tamias striatus) is embedded within H. arboricola, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within H. arboricola, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.
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Affiliation(s)
- Kayce C Bell
- Mammalogy Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA; Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA.
| | - Julie M Allen
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - Joseph A Cook
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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9
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Phylogeography of the Volcano Rabbit (Romerolagus diazi): the Evolutionary History of a Mountain Specialist Molded by the Climatic-Volcanism Interaction in the Central Mexican Highlands. J MAMM EVOL 2020. [DOI: 10.1007/s10914-019-09493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Bell KC, Demboski JR, Cook JA. Sympatric Parasites Have Similar Host-Associated, but Asynchronous, Patterns of Diversification. Am Nat 2018; 192:E106-E119. [DOI: 10.1086/698300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Sarver BAJ, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias). Genome Biol Evol 2018; 9:7-19. [PMID: 28172670 PMCID: PMC5381575 DOI: 10.1093/gbe/evw254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 11/16/2022] Open
Abstract
Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.
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Affiliation(s)
- Brice A J Sarver
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO.,Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Nicholas Forshee
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
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12
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Frare CF, Matocq MD, Feldman CR, White AM, Manley PN, Jermstad KD, Hekkala ER. Landscape disturbance and sporadic hybridization complicate field identification of chipmunks. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Chris R. Feldman
- University of Nevada; Reno, 1664 N. Virginia St. Reno NV 89557 USA
| | - Angela M. White
- Pacific Southwest Research Station; 1731 Research Park Drive Davis CA 95618 USA
| | - Patricia N. Manley
- Pacific Southwest Research Station; 2480 Carson Road Placerville CA 95667 USA
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13
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Bell KC, Calhoun KL, Hoberg EP, Demboski JR, Cook JA. Temporal and spatial mosaics: deep host association and shallow geographic drivers shape genetic structure in a widespread pinworm, Rauschtineria eutamii. Biol J Linn Soc Lond 2016; 119:397-413. [PMID: 27725785 PMCID: PMC5055073 DOI: 10.1111/bij.12833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Climate and host demographic cycling often shape both parasite genetic diversity and host distributions, processes that transcend a history of strict host-parasite association. We explored host associations and histories based on an evaluation of mitochondrial and nuclear sequences to reveal the underlying history and genetic structure of a pinworm, Rauschtineria eutamii, infecting 10 species of western North American chipmunks (Rodentia:Tamias, subgenus Neotamias). Rauschtineria eutamii contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic R. eutamii mitochondrial clades, largely supported by nuclear gene trees, exhibiting divergence levels comparable to intraspecific variation reported for other nematodes. Phylogenetic relationships among pinworm clades suggest that R. eutamii colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging Neotamias species or species groups. Pinworm diversification, however, is incongruent and asynchronous relative to host diversification. Secondarily, patterns of shallow divergence were shaped by geography through events of episodic colonization reflecting an interaction of taxon pulses and ecological fitting among assemblages in recurrent sympatry. Pinworms occasionally infect geographically proximal host species; however, host switching may be unstable or ephemeral, as there is no signal of host switching in the deeper history of R. eutamii.
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Affiliation(s)
- Kayce C. Bell
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87108, USA
| | - Kendall L. Calhoun
- Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, California 94720, USA
| | - Eric P. Hoberg
- US National Parasite Collection, USDA, Agricultural Research Service, Beltsville Area Research Center, BARC East 1180, 10300 Baltimore Avenue, Beltsville, Maryland 20715, USA
| | - John R. Demboski
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, Colorado 80205, USA
| | - Joseph A. Cook
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87108, USA
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Lowrey C, Longshore K, Riddle B, Mantooth S. Ecology, distribution, and predictive occurrence modeling of Palmer’s chipmunk (Tamias palmeri): a high-elevation small mammal endemic to the Spring Mountains in southern Nevada, USA. J Mammal 2016. [DOI: 10.1093/jmammal/gyw026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Although montane sky islands surrounded by desert scrub and shrub steppe comprise a large part of the biological diversity of the Basin and Range Province of southwestern North America, comprehensive ecological and population demographic studies for high-elevation small mammals within these areas are rare. Here, we examine the ecology and population parameters of the Palmer’s chipmunk (Tamias palmeri) in the Spring Mountains of southern Nevada, and present a predictive GIS-based distribution and probability of occurrence model at both home range and geographic spatial scales. Logistic regression analyses and Akaike Information Criterion model selection found variables of forest type, slope, and distance to water sources as predictive of chipmunk occurrence at the geographic scale. At the home range scale, increasing population density, decreasing overstory canopy cover, and decreasing understory canopy cover contributed to increased survival rates.
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15
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Patterson BD, Norris RW. Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks. MAMMALIA 2016. [DOI: 10.1515/mammalia-2015-0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe chipmunks are a Holarctic group of ground squirrels currently allocated to the genus
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Vander Wall SB, Jenkins SH. Plant—animal interactions and climate: Why do yellow pine chipmunks (Tamias amoenus) and eastern chipmunks (Tamias striatus) have such different effects on plants? ECOSCIENCE 2015. [DOI: 10.2980/18-2-3375] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Bell KC, Matek D, Demboski JR, Cook JA. Expanded Host Range of Sucking Lice and Pinworms of Western North American Chipmunks. COMP PARASITOL 2015. [DOI: 10.1654/4756.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Bueno-Silva M, Boeger WA. Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids. Folia Parasitol (Praha) 2014; 61:213-22. [PMID: 25065127 DOI: 10.14411/fp.2014.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Based on molecular markers (COII and ITS1-ITS2) and morphological data, we describe three new Neotropical species of Gyrodactylus von Nordmann, 1832 from Scleromystax barbatus (Quoy et Gaimard) and Scleromystax macropterus (Regan) from southern Brazil. The three new species can be distinguished from each other by sequences of both molecular markers and morphology of hooks and anchors. Gyrodactylus bueni sp. n. is characterised by having hook with shaft curved, heel straight, shelf straight, toe pointed, anchor with superficial root slender, elongate and male copulatory organ armed with two rows of spinelets. Gyrodactylus major sp. n. presents hook with shaft, point curved, proximal shaft straight, heel convex, shelf convex, toe concave, anchor with superficial root robust and male copulatory organ armed with two rows of spinelets. Gyrodactylus scleromystaci sp. n. presents hook with shaft, point recurved, heel convex, shelf convex, toe pointed, anchor with superficial root curved and male copulatory organ armed with two rows of spinelets. These species appear to be closely related to other species of Gyrodactylus known from other species of Callichthyidae. These new species, however, differ by the comparative morphology of the haptoral hard structures and molecular data. Comparative analysis of sequences from these species of Gyrodactylus suggests that the COII gene may represent an important marker for the taxonomy of species of Gyrodactylidae and, perhaps, for species of other lineages of Monogenoidea.
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Yin LF, Wang F, Zhang Y, Kuang H, Schnabel G, Li GQ, Luo CX. Evolutionary analysis revealed the horizontal transfer of the Cyt b gene from Fungi to Chromista. Mol Phylogenet Evol 2014; 76:155-61. [DOI: 10.1016/j.ympev.2014.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/06/2014] [Accepted: 03/15/2014] [Indexed: 01/21/2023]
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20
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Sullivan J, Demboski JR, Bell KC, Hird S, Sarver B, Reid N, Good JM. Divergence with gene flow within the recent chipmunk radiation (Tamias). Heredity (Edinb) 2014; 113:185-94. [PMID: 24781803 DOI: 10.1038/hdy.2014.27] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/08/2014] [Accepted: 01/17/2014] [Indexed: 12/25/2022] Open
Abstract
Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.
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Affiliation(s)
- J Sullivan
- 1] Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA [2] BEACON Center for the Study of Evolution in Action
| | - J R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
| | - K C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - S Hird
- Department of Biological Sciences and Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - B Sarver
- 1] Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA [2] BEACON Center for the Study of Evolution in Action
| | - N Reid
- Department of Biological Sciences and Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - J M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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21
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Rubidge EM, Patton JL, Moritz C. Diversification of the Alpine chipmunk, Tamias alpinus, an alpine endemic of the Sierra Nevada, California. BMC Evol Biol 2014; 14:34. [PMID: 24559294 PMCID: PMC4077034 DOI: 10.1186/1471-2148-14-34] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The glaciation cycles that occurred throughout the Pleistocene in western North America caused frequent shifts in species' ranges with important implications for models of species divergence. For example, long periods of allopatry during species' range contractions allowed for the accumulation of differences between separated populations promoting lineage divergence. In contrast, range expansions during interglacial periods may have had homogenizing effects via increased gene flow following secondary contact. These range dynamics are particularly pronounced in the Sierra Nevada, California, given the complex topography and climatic history of the area, thus providing a natural laboratory to examine evolutionary processes that have led to the diversity patterns observed today. RESULTS Here we examined the role of late Pleistocene climate fluctuations on the divergence of the Sierra Nevada endemic Alpine Chipmunk (Tamias alpinus) from its sister taxon, western populations of the Least Chipmunk (T. minimus) from the Great Basin. We used one mitochondrial gene (cytochrome b) and 14 microsatellite loci to examine the evolutionary relationship between these species. Mitochondrial sequence data revealed that T. alpinus and T. minimus populations share mitochondrial haplotypes with no overall geneaological separation, and that diversity at this locus is better explained by geography than by species' boundaries. In contrast, the microsatellite analysis showed that populations of the same species are more similar to each other than they are to members of the other species. Similarly, a morphological analysis of voucher specimens confirmed known differences in morphological characters between species providing no evidence of recent hybridization. Coalescent analysis of the divergence history indicated a late Pleistocene splitting time (~450 ka) and subsequent, though limited, gene flow between the two lineages. CONCLUSIONS Our results suggest that the two species are distinct and there is no contemporary introgression along their geographic boundary. The divergence of T. alpinus during this time period provides additional evidence that Pleistocene glacial cycles played an important role in diversification of species in Sierra Nevada and North America in general.
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Affiliation(s)
- Emily M Rubidge
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building University of California, Berkeley, California 94720-3160, USA.
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Ge DY, Liu X, Lv XF, Zhang ZQ, Xia L, Yang QS. Historical Biogeography and Body Form Evolution of Ground Squirrels (Sciuridae: Xerinae). Evol Biol 2013. [DOI: 10.1007/s11692-013-9250-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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McKelvey KS, Ramirez JE, Pilgrim KL, Cushman SA, Schwartz MK. Genetic Sampling of Palmer's Chipmunks in the Spring Mountains, Nevada. WEST N AM NATURALIST 2013. [DOI: 10.3398/064.073.0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Piaggio AJ, Coghlan BA, Miscampbell AE, Arjo WM, Ransome DB, Ritland CE. Molecular phylogeny of an ancient rodent family (Aplodontiidae). J Mammal 2013. [DOI: 10.1644/12-mamm-a-016.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Patterson BD. Book review: Squirrels of the World. Richard W. Thorington, Jr., John L. Koprowski, Michael A. Steele, and James F. Whatton. 2012. Johns Hopkins University Press, Baltimore, 459 pp. $75.00 (hardbound) ISBN: 978-1-4214-0469-1. J Wildl Manage 2013. [DOI: 10.1002/jwmg.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yin LF, Hu MJ, Wang F, Kuang H, Zhang Y, Schnabel G, Li GQ, Luo CX. Frequent gain and loss of introns in fungal cytochrome b genes. PLoS One 2012; 7:e49096. [PMID: 23145081 PMCID: PMC3492308 DOI: 10.1371/journal.pone.0049096] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022] Open
Abstract
In this study, all available cytochrome b (Cyt b) genes from the GOBASE database were compiled and the evolutionary dynamics of the Cyt b gene introns was assessed. Cyt b gene introns were frequently present in the fungal kingdom and some lower plants, but generally absent or rare in Chromista, Protozoa, and Animalia. Fungal Cyt b introns were found at 35 positions in Cyt b genes and the number of introns varied at individual positions from a single representative to 32 different introns at position 131, showing a wide and patchy distribution. Many homologous introns were present at the same position in distantly related species but absent in closely related species, suggesting that introns of the Cyt b genes were frequently lost. On the other hand, highly similar intron sequences were observed in some distantly related species rather than in closely related species, suggesting that these introns were gained independently, likely through lateral transfers. The intron loss-and-gain events could be mediated by transpositions that might have occurred between nuclear and mitochondria. Southern hybridization analysis confirmed that some introns contained repetitive sequences and might be transposable elements. An intron gain in Botryotinia fuckeliana prevented the development of QoI fungicide resistance, suggesting that intron loss-and-gain events were not necessarily beneficial to their host organisms.
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Affiliation(s)
- Liang-Fen Yin
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Meng-Jun Hu
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Fei Wang
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Hanhui Kuang
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yu Zhang
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Guido Schnabel
- School of Agricultural, Forestry & Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Guo-Qing Li
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Chao-Xi Luo
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, People’s Republic of China
- * E-mail:
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Reid N, Demboski JR, Sullivan J. Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Syst Biol 2011; 61:44-62. [PMID: 21878471 DOI: 10.1093/sysbio/syr094] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: Neotamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion.
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Affiliation(s)
- Noah Reid
- Department of Biological Sciences, Room 105, Louisiana State University, Baton Rouge, LA 70803, USA.
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Kartavtsev YP. Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genomics 2011; 4:71-81. [DOI: 10.1016/j.margen.2011.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 01/26/2011] [Accepted: 02/23/2011] [Indexed: 11/15/2022]
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Chang SW, Oshida T, Endo H, Nguyen ST, Dang CN, Nguyen DX, Jiang X, Li ZJ, Lin LK. Ancient hybridization and underestimated species diversity in Asian striped squirrels (genus Tamiops): inference from paternal, maternal and biparental markers. J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00822.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Angert AL, Crozier LG, Rissler LJ, Gilman SE, Tewksbury JJ, Chunco AJ. Do species’ traits predict recent shifts at expanding range edges? Ecol Lett 2011; 14:677-89. [DOI: 10.1111/j.1461-0248.2011.01620.x] [Citation(s) in RCA: 397] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lammers AR, Zurcher U. Torque around the center of mass: dynamic stability during quadrupedal arboreal locomotion in the Siberian chipmunk (Tamias sibiricus). ZOOLOGY 2011; 114:95-103. [DOI: 10.1016/j.zool.2010.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 09/24/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
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Huang KM, Liu SM, Chen YJ, Huang YW, Deng JF, Hwang DF. Identification of causative agents and species in shrimp implicated in a food poisoning case in Taiwan. J Food Prot 2010; 73:2250-5. [PMID: 21219744 DOI: 10.4315/0362-028x-73.12.2250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The possible causative agent and shrimp species involved in a bait shrimp poisoning case that occurred in northern Taiwan was determined. Because the patient's symptoms were similar to those caused by boric acid and slightly similar to those caused by sulfite, the concentrations of boric acid and sulfite (as sulfur dioxide) in the patient's vomitus and in shrimp collected from bait stores and markets were analyzed. The concentration of boric acid was 36.8 to 37.1 mg/g in the patient's vomitus, 1.4 to 3.8 mg/g in shrimp meats obtained from bait stores, and not detectable (less than 0.001 mg/g) in shrimp meat obtained from commercial markets. No significant differences in sulfur dioxide concentrations (0.067 to 0.088 mg/g) were found in patient's vomitus and the shrimp meat from both bait stores and commercial markets. A fragment of the cytochrome b gene (∼406 bp) was amplified by PCR using a pair of primers (UCYTB151F and UCYTB270R) from shrimp meat of two species and the vomitus. The vomited shrimp was identified as Parapenaeus fissuroides on the basis of gene sequencing and restriction fragment length polymorphism patterns after treatment with endonuclease Alu I. Based on the patient's symptoms and analytical data, we concluded that boric acid at toxic levels had been illegally added to the bait shrimp P. fissuroides.
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Affiliation(s)
- Ken-Men Huang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan, Republic of China
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Clucas B, Ord TJ, Owings DH. Fossils and phylogeny uncover the evolutionary history of a unique antipredator behaviour. J Evol Biol 2010; 23:2197-2211. [PMID: 20840310 DOI: 10.1111/j.1420-9101.2010.02083.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently, two squirrel species (Spermophilus spp.) were discovered to anoint their bodies with rattlesnake scent as a means of concealing their odour from these chemosensory predators. In this study, we tested multiple species with predator scents (rattlesnake and weasel) to determine the prevalence of scent application across the squirrel phylogeny. We reconstructed the evolutionary history of the behaviour using a phylogenetic analysis and fossil records of historic predator co-occurrence. Squirrels with historical and current rattlesnake co-occurrence all applied rattlesnake scent, whereas no relationship existed between weasel scent application and either weasel or rattlesnake co-occurrence. This was surprising because experimental tests confirmed rattlesnake and weasel scent were both effective at masking prey odour from hunting rattlesnakes (the primary predator of squirrels). Ancestral reconstructions and fossil data suggest predator scent application in squirrels is ancient in origin, arising before co-occurrences with rattlesnakes or weasels in response to some other, now extinct, chemosensory predator.
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Affiliation(s)
- B Clucas
- College of The Environment, University of Washington, Seattle, WA 98195, USA.
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Koh HS, Zhang M, Bayarlkhagva D, Ham EJ, Kim JS, Jang KH, Park NJ. Concordant genetic distinctness of the phylogroup of the Siberian chipmunk from the Korean peninsula (Tamias sibiricus barberi), reexamined with nuclear DNA c-myc gene exon 2 and mtDNA control region sequences. Biochem Genet 2010; 48:696-705. [PMID: 20526736 DOI: 10.1007/s10528-010-9352-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 03/29/2010] [Indexed: 10/19/2022]
Abstract
We reexamined Tamias sibiricus barberi from Korea by sequencing c-myc exon 2 and the mtDNA control region. In the c-myc exon, the monogenic T. s. barberi differed from the monogenic T. s. orientalis (nucleotide distance 0.48%; 3 variable sites at 168, 306, and 552), whereas T. s. orientalis was identical to T. s. sibiricus. In the control region, T. s. barberi differed from T. s. orientalis (distance 6.84%) and T. s. sibiricus (9.35%). We considered the concordant, extensive gaps between the phylogroup of T. s. barberi and other subspecies of T. sibiricus in the c-myc gene, control region, and cytochrome b gene to be evidence of a lack of intergradation through North Korea from T. s. barberi to T. s. orientalis. Our results, showing the genetic and morphological distinctness of T. s. barberi, support that this phylogroup is a distinct species.
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Affiliation(s)
- Hung Sun Koh
- Department of Biology, Chungbuk University, Cheongju, Korea.
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Altaba CR. Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws. PLoS One 2009; 4:e4611. [PMID: 19242549 PMCID: PMC2644784 DOI: 10.1371/journal.pone.0004611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? METHODOLOGY In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. PRINCIPAL FINDINGS All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. SIGNIFICANCE There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.
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Affiliation(s)
- Cristian R Altaba
- Laboratory of Human Systematics, University of the Balearic Islands, Balearic Islands, Spain.
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Obolenskaya EV, Lee MY, Dokuchaev NE, Oshida T, Lee MS, Lee H, Lissovsky AA. Diversity of Palaearctic chipmunks (Tamias, Sciuridae). MAMMALIA 2009. [DOI: 10.1515/mamm.2009.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Koh HS, Wang J, Lee BK, Yang BG, Heo SW, Jang KH, Chun TY. A Phylogroup of the Siberian Chipmunk from Korea (Tamias sibiricus barberi) Revealed from the Mitochondrial DNA Cytochrome b Gene. Biochem Genet 2008; 47:1-7. [DOI: 10.1007/s10528-008-9200-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 07/15/2008] [Indexed: 11/29/2022]
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Hayssen V. Reproduction within marmotine ground squirrels (Sciuridae, Xerinae, Marmotini): patterns among genera. J Mammal 2008. [DOI: 10.1644/07-mamm-a-218r1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J. Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol Ecol 2008; 17:1313-27. [PMID: 18302691 DOI: 10.1111/j.1365-294x.2007.03640.x] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks (Tamias ruficaudus and T. amoenus). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus, T. a. canicaudus, with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus. Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.
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Affiliation(s)
- Jeffrey M Good
- Department of Ecology and Evolutionary Biology, University of Arizona, Biosciences West, Tucson, AZ 85721, USA
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Davis EB, Koo MS, Conroy C, Patton JL, Moritz C. The California Hotspots Project: identifying regions of rapid diversification of mammals. Mol Ecol 2008; 17:120-38. [PMID: 17725571 DOI: 10.1111/j.1365-294x.2007.03469.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high rate of anthropogenic impact on natural systems mandates protection of the evolutionary processes that generate and sustain biological diversity. Environmental drivers of diversification include spatial heterogeneity of abiotic and biotic agents of divergent selection, features that suppress gene flow, and climatic or geological processes that open new niche space. To explore how well such proxies perform as surrogates for conservation planning, we need first to map areas with rapid diversification -'evolutionary hotspots'. Here we combine estimates of range size and divergence time to map spatial patterns of neo-endemism for mammals of California, a global biodiversity hotspot. Neo-endemism is explored at two scales: (i) endemic species, weighted by the inverse of range size and mtDNA sequence divergence from sisters; and (ii) as a surrogate for spatial patterns of phenotypic divergence, endemic subspecies, again using inverse-weighting of range size. The species-level analysis revealed foci of narrowly endemic, young taxa in the central Sierra Nevada, northern and central coast, and Tehachapi and Peninsular Ranges. The subspecies endemism-richness analysis supported the last four areas as hotspots for diversification, but also highlighted additional coastal areas (Monterey to north of San Francisco Bay) and the Inyo Valley to the east. We suggest these hotspots reflect the major processes shaping mammal neo-endemism: steep environmental gradients, biotic admixture areas, and areas with recent geological/climate change. Anthropogenic changes to both environment and land use will have direct impacts on regions of rapid divergence. However, despite widespread changes to land cover in California, the majority of the hotspots identified here occur in areas with relatively intact ecological landscapes. The geographical scope of conserving evolutionary process is beyond the scale of any single agency or nongovernmental organization. Choosing which land to closely protect and/or purchase will always require close coordination between agencies.
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Affiliation(s)
- Edward Byrd Davis
- University of California Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
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Lin WF, Hwang DF. Application of species-specific PCR for the identification of dried bonito product (Katsuobushi). Food Chem 2008. [DOI: 10.1016/j.foodchem.2007.05.060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fitzpatrick BM, Turelli M. THE GEOGRAPHY OF MAMMALIAN SPECIATION: MIXED SIGNALS FROM PHYLOGENIES AND RANGE MAPS. Evolution 2007. [DOI: 10.1111/j.0014-3820.2006.tb01140.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Benjamin M. Fitzpatrick
- Section of Evolution and Ecology and Center for Population Biology University of California, Davis, California 95616
| | - Michael Turelli
- Section of Evolution and Ecology and Center for Population Biology University of California, Davis, California 95616
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Banbury JL, Spicer GS. Molecular Systematics of Chipmunks (Neotamias) Inferred by Mitochondrial Control Region Sequences. J MAMM EVOL 2007. [DOI: 10.1007/s10914-006-9035-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rowe KC, Heske EJ, Paige KN. Comparative phylogeography of eastern chipmunks and white-footed mice in relation to the individualistic nature of species. Mol Ecol 2006; 15:4003-20. [PMID: 17054499 DOI: 10.1111/j.1365-294x.2006.03063.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Palaeoecological studies have demonstrated that ecological communities as a whole did not remain stable throughout the climatic fluctuations of the Quaternary. The result is that long-term associations of species cannot be inferred by contemporary associations in ecological communities. Therefore, the evolutionary significance of any contemporary ecological interactions among species and of the biotic community within which species have evolved also cannot be assumed from contemporary conditions. Comparative phylogeographic data provide a method to identify species within ecological communities that have shared biogeographic histories. We present an example of a long-term association between populations of two mammalian species, eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus), which are commonly associated with deciduous forest habitats. The distribution of mitochondrial DNA variation in T. striatus and P. leucopus from previously glaciated regions of the eastern United States support the hypothesis that, in at least part of their range, genetic lineages of the two species have expanded from similar population sources since the Last Glacial Maximum. In addition, the spatial concordance of genetic lineages of T. striatus and P. leucopus with the oak-savannah forest formations of Wisconsin and Illinois, suggest that populations associated with this community colonized the area in association with a set of arboreal species that comprise their deciduous forest habitat.
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Affiliation(s)
- Kevin C Rowe
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-1100, USA.
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Kartavtsev YP, Lee JS. Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406040016] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fitzpatrick BM, Turelli M. THE GEOGRAPHY OF MAMMALIAN SPECIATION: MIXED SIGNALS FROM PHYLOGENIES AND RANGE MAPS. Evolution 2006. [DOI: 10.1554/05-453.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kizirian D, Donnelly MA. The criterion of reciprocal monophyly and classification of nested diversity at the species level. Mol Phylogenet Evol 2005; 32:1072-6. [PMID: 15288076 DOI: 10.1016/j.ympev.2004.05.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2003] [Revised: 03/07/2004] [Indexed: 11/22/2022]
Affiliation(s)
- David Kizirian
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
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