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Ji J, Jackson DJ, Leaché AD, Yang Z. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks. Syst Biol 2023; 72:446-465. [PMID: 36504374 PMCID: PMC10275556 DOI: 10.1093/sysbio/syac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 10/25/2023] Open
Abstract
In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].
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Affiliation(s)
- Jiayi Ji
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Donavan J Jackson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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2
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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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3
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UCE sequencing-derived mitogenomes reveal the timing of mitochondrial replacement in Malagasy shrew tenrecs (Afrosoricida, Tenrecidae, Microgale). Mamm Biol 2022. [DOI: 10.1007/s42991-022-00246-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractMalagasy shrew tenrecs (Microgale) have increasingly been used to study speciation genetics over the last years. A previous study recently uncovered gene flow between the Shrew-toothed shrew tenrec (M. soricoides) and sympatric southern population of the Pale shrew tenrec (M. fotsifotsy). This gene flow has been suggested to be accompanied by complete mitochondrial replacement in M. fotsifotsy. To explore the temporal framework of this replacement, we assembled mitogenomes from publicly available sequencing data of ultra-conserved elements. We were able to assemble complete and partial mitogenomes for 19 specimens from five species of shrew tenrecs, which represents a multifold increase in mitogenomic resources available for all tenrecs. Phylogenetic inferences and sequence simulations support the close relationship between the mitochondrial lineages of M. soricoides and the southern population of M. fotsifotsy. Based on the nuclear divergence of northern and southern populations of M. fotsifotsy and the mitochondrial divergence between the latter and M. soricoides, there was a mean time window for replacement of ~ 350,000 years. This timeframe implies that the effective size of the ancestral M. fotsifotsy southern population was less 70,000.
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4
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McLean BS, Bell KC, Cook JA. SNP-based Phylogenomic Inference in Holarctic Ground Squirrels (Urocitellus). Mol Phylogenet Evol 2022; 169:107396. [PMID: 35031463 DOI: 10.1016/j.ympev.2022.107396] [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: 08/04/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022]
Abstract
Resolution of rapid evolutionary radiations requires harvesting maximal signal from phylogenomic datasets. However, studies of non-model clades often target conserved loci that are characterized by reduced information content, which can negatively affect gene tree precision and species tree accuracy. Single nucleotide polymorphism (SNP)-based methods are an underutilized but potentially valuable tool for estimating phylogeny and divergence times because they do not rely on resolved gene trees, allowing information from many or all variant loci to be leveraged in species tree reconstruction. We evaluated the utility of SNP-based methods in resolving phylogeny of Holarctic ground squirrels (Urocitellus), a radiation that has been difficult to disentangle, even in prior phylogenomic studies. We inferred phylogeny from a dataset of >3,000 ultraconserved element loci (UCEs) using two methods (SNAPP, SVDquartets) and compared our results with a new mitogenome phylogeny. We also systematically evaluated how phasing of UCEs improves per-locus information content, and inference of topology and other parameters within each of these SNP-based methods. Phasing improved topological resolution and branch length estimation at shallow levels (within species complexes), but less so at deeper levels, likely reflecting true uncertainty due to ancestral polymorphisms segregating in these rapidly diverging lineages. We resolved several key clades in Urocitellus and present targeted opportunities for future phylogenomic inquiry. Our results extend the roadmap for use of SNPs to address vertebrate radiations and support comparative analyses at multiple temporal scales.
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Affiliation(s)
- Bryan S McLean
- University of North Carolina Greensboro, Department of Biology, Greensboro, NC 27402 USA.
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, Department of Mammalogy, Los Angeles, CA 90007 USA.
| | - Joseph A Cook
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM 87131 USA.
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5
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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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6
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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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7
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Puckett EE, Murphy SM, Bradburd G. Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. Ecol Evol 2021; 11:12114-12128. [PMID: 34522364 PMCID: PMC8427584 DOI: 10.1002/ece3.7975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiation and distinctiveness of the N. m. atristriatus population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of N. minimus genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.6 and 8.5 scenarios. We identified three geographically structured groups (West, North, and South) that were supported by both mitochondrial and nuclear data. N. m. atristriatus grouped within a unique South subclade but were not reciprocally monophyletic from N. m. operarius, and nuclear genome analyses did not separate N. m. atristriatus, N. m. caryi, and N. m. operarius. Thus, while least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported and listing of the Peñasco population as a Distinct Population Segment of N. m. operarius may be warranted. Our results also support consideration of populations with North and West mitogenomes as two additional evolutionary significant units. We found that N. minimus genetic diversity declined by ~87% over the last century, and our models predicted substantial future habitat contraction, including the loss of the full contemporary ranges of N. m. atristriatus, N. m. arizonensis, and N. m. chuskaensis.
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Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Sean M. Murphy
- Wildlife Management DivisionNew Mexico Department of Game & FishSanta FeNew MexicoUSA
- Present address:
Department of Forestry and Natural ResourcesUniversity of KentuckyLexingtonKentuckyUSA
| | - Gideon Bradburd
- Department of Integrative BiologyEcology, Evolution, and Behavior GroupMichigan State UniversityEast LansingMichiganUSA
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8
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Bell KC, Van Gunst J, Teglas MB, Hsueh J, Matocq MD. Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of Tamias amoenus. J Mammal 2021; 102:173-187. [DOI: 10.1093/jmammal/gyaa166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (Tamias amoenus celeris), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled T. amoenus and least chipmunks (T. minimus) from the isolated PFR and compared genetic diversity between these populations and more “mainland” populations, including other subspecies of chipmunks. Given the high frequency of hybridization in Tamias, we tested for hybridization between T. amoenus and T. minimus in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, Borrelia hermsii, to gain insight into population health. We found T. amoenus of the PFR are closely related to T. amoenus in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR T. amoenus are highly genetically differentiated from other populations. In contrast, PFR T. minimus had higher genetic diversity that was comparable to the other T. minimus population we sampled. Pathogen screening revealed that T. amoenus carried higher pathogen loads than T. minimus in the PFR, although the prevalence of infection was similar to other Tamias populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.
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Affiliation(s)
- Kayce C Bell
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, USA
| | | | - Mike B Teglas
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Mail Stop 202, Reno, NV USA
| | - Jennifer Hsueh
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Mail Stop 202, Reno, NV USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, University of Nevada, Mail Stop 186, Reno, NV, USA
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9
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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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10
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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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11
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Menéndez I, Gómez Cano AR, Cantalapiedra JL, Peláez‐Campomanes P, Álvarez‐Sierra MÁ, Hernández Fernández M. A multi‐layered approach to the diversification of squirrels. Mamm Rev 2020. [DOI: 10.1111/mam.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | | | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, GloCEE Global Change Ecology and Evolution Research Group Universidad de Alcalá Plaza de San Diego s/n, Alcalá de Henares Madrid28801 Spain
| | - Pablo Peláez‐Campomanes
- Departameto de Paleobiología Museo Nacional de Ciencias Naturales, MNCN‐CSIC C/ José Gutiérrez Abascal, 2 Madrid28006 Spain
| | - María Ángeles Álvarez‐Sierra
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas Universidad Complutense de Madrid C/ José Antonio Novais 12 Madrid28040 Spain
- Departamento de Cambio Medioambiental Instituto de Geociencias (UCM, CSIC) C/Severo Ochoa 7 Madrid28040 Spain
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12
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Simon C. An Evolving View of Phylogenetic Support. Syst Biol 2020; 71:921-928. [PMID: 32915964 DOI: 10.1093/sysbio/syaa068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
If all nucleotide sites evolved at the same rate within molecules and throughout the history of lineages, if all nucleotides were in equal proportion, if any nucleotide or amino acid evolved to any other with equal probability, if all taxa could be sampled, if diversification happened at well-spaced intervals, and if all gene segments had the same history, then tree building would be easy. But of course none of those conditions are true. Hence the need for evaluating the information content and accuracy of phylogenetic trees. The symposium for which this historial essay and presentation were developed focused on the importance of phylogenetic support, specifically branch support for individual clades. Here I present a timeline and review significant events in the history of systematics that set the stage for the development of the sophisticated measures of branch support and examinations of the information content of data highlighted in this symposium.
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Affiliation(s)
- Chris Simon
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Road, University of Connecticut, Storrs, CT
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13
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Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM. No evidence for phylosymbiosis in western chipmunk species. FEMS Microbiol Ecol 2020; 96:5626339. [PMID: 31730167 DOI: 10.1093/femsec/fiz182] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.
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Affiliation(s)
- Kirsten Grond
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA
| | - Kayce C Bell
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave, NW, Washington, DC, 20560, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, 2001 Colorado Blvd, Denver, CO, 80205, USA
| | - Malia Santos
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Jack M Sullivan
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Sarah M Hird
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA.,Institute of Systems Genomics, University of Connecticut, 67 N Eagleville Rd, Storrs, CT, 06269, USA
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14
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Pulido‐Santacruz P, Aleixo A, Weir JT. Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation*. Evolution 2020; 74:842-858. [DOI: 10.1111/evo.13902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Paola Pulido‐Santacruz
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
- Current address: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Calle 28A No. 15 – 09 Bogotá Colombia
| | | | - Jason T. Weir
- Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
- Department of Biological SciencesUniversity of Toronto Scarborough Toronto Canada
- Department of OrnithologyRoyal Ontario Museum Toronto Canada
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15
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Duckett DJ, Pelletier TA, Carstens BC. Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP. PeerJ 2020; 8:e8271. [PMID: 31949994 PMCID: PMC6956792 DOI: 10.7717/peerj.8271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.
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Affiliation(s)
- Drew J Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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16
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Hope AG, Stephens RB, Mueller SD, Tkach VV, Demboski JR. Speciation of North American pygmy shrews (Eulipotyphla: Soricidae) supports spatial but not temporal congruence of diversification among boreal species. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractSpeciation among many animals was rapid through the Pleistocene, impacted by climate and periodic isolation and reconnection. As such, species limits among often morphologically cryptic lineages may remain unresolved despite clear mitogenomic partitioning. Accumulating evidence from phylogeographical studies is revealing congruent regional differentiation of lineages across taxonomic groups that share ecological and evolutionary traits. Here, we analyse multiple DNA loci and morphology to resolve the geography and timeframe associated with evolutionary history of North American pygmy shrews (genus Sorex). We then assess lineage diversification among three co-distributed shrew complexes using phylogenetic and approximate Bayesian computation approaches to test a hypothesis of spatial congruence but temporal incongruence of species formation on a continental scale. Our results indicate consistency in regional lineage distributions, partial congruence of the sequence of divergence, and strong but not definitive support for temporal incongruence, suggesting that successive glacial cycles initiated the process of diversification repeatedly through the Pleistocene. Our results emphasize a continuing need for greater genomic coverage in comparative phylogeography, with persistent challenges. We recognize distinct eastern (Sorex hoyi Baird, 1857) and western (Sorex eximius Osgood, 1901) species of pygmy shrew based on available evidence, but discuss issues with taxonomic designations considering the continuum of speciation throughout the boreal biome.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, 116 Ackert Hall, Kansas State University, Manhattan, KS, USA
| | - Ryan B Stephens
- Natural Resources and the Environment, 114 James Hall, University of New Hampshire, Durham, NH, USA
| | | | - Vasyl V Tkach
- Department of Biology, Starcher Hall, University of North Dakota Grand Forks, Grand Forks, ND, USA
| | - John R Demboski
- Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, CO, USA
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17
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Reis CA, Dias C, Araripe J, Aleixo A, Anciães M, Sampaio I, Schneider H, Rêgo PS. Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance. ZOOL SCR 2019. [DOI: 10.1111/zsc.12395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Camila Alves Reis
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Cleyssian Dias
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Juliana Araripe
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Marina Anciães
- Laboratório de Evolução e Comportamento Animal COBIO Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Horacio Schneider
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Péricles Sena Rêgo
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
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18
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Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM. Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genet 2019; 15:e1008119. [PMID: 31050681 PMCID: PMC6519841 DOI: 10.1371/journal.pgen.1008119] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 05/15/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022] Open
Abstract
Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911-2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments.
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Affiliation(s)
- Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, United States of America
| | - Tyler Linderoth
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, Australia
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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19
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Mclean BS, Bell KC, Allen JM, Helgen KM, Cook JA. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Syst Biol 2018; 68:298-316. [DOI: 10.1093/sysbio/syy064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Bryan S Mclean
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Department of Invertebrate Zoology, Smithsonian Institution National Museum of Natural History, P.O. Box 37012, MRC 163, Washington, DC 20013-7012, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Kristofer M Helgen
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
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20
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Bono JM, Pigage HK, Wettstein PJ, Prosser SA, Pigage JC. Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group. BMC Evol Biol 2018; 18:139. [PMID: 30208839 PMCID: PMC6134581 DOI: 10.1186/s12862-018-1248-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 01/09/2023] Open
Abstract
Background Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert’s squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. Results We used RAD-seq to unravel the complex evolutionary history of the Abert’s squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. Conclusions Overall, the evolutionary history of Abert’s squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories. Electronic supplementary material The online version of this article (10.1186/s12862-018-1248-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
| | - Helen K Pigage
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Peter J Wettstein
- Department of Surgery, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA
| | - Stephanie A Prosser
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Jon C Pigage
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
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21
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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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22
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Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae). Mol Phylogenet Evol 2018; 126:314-320. [DOI: 10.1016/j.ympev.2018.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 04/04/2018] [Accepted: 04/11/2018] [Indexed: 11/19/2022]
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23
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Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes. Commun Biol 2018; 1:51. [PMID: 30271934 PMCID: PMC6123727 DOI: 10.1038/s42003-018-0058-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/20/2018] [Indexed: 01/19/2023] Open
Abstract
At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence. Jocelyn Colella et al. report whole-genome sequences of 10 stoats (Mustela erminea) from four regions of glacial refugia. They find evidence for two past introgressive events between lineages that coincide with interglacial periods, a pattern that may extend to other high–latitude species.
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24
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Morales AE, Carstens BC. Evidence that Myotis lucifugus “Subspecies” are Five Nonsister Species, Despite Gene Flow. Syst Biol 2018; 67:756-769. [DOI: 10.1093/sysbio/syy010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ariadna E Morales
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
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25
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Folk RA, Mandel JR, Freudenstein JV. Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms. Syst Biol 2018; 66:320-337. [PMID: 27637567 DOI: 10.1093/sysbio/syw083] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/04/2016] [Indexed: 11/12/2022] Open
Abstract
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].
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Affiliation(s)
- Ryan A Folk
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA and
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - John V Freudenstein
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA and
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26
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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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27
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Banker SE, Wade EJ, Simon C. The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia. Mol Phylogenet Evol 2017; 116:172-181. [DOI: 10.1016/j.ympev.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/04/2017] [Accepted: 08/17/2017] [Indexed: 01/28/2023]
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28
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Bohn SJ, Webber QMR, Florko KRN, Paslawski KR, Peterson AM, Piche JE, Menzies AK, Willis CKR. Personality predicts ectoparasite abundance in an asocial sciurid. Ethology 2017. [DOI: 10.1111/eth.12651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shelby J. Bohn
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Quinn M. R. Webber
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Katie R. N. Florko
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Katlyn R. Paslawski
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Amelia M. Peterson
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Julia E. Piche
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Allyson K. Menzies
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
| | - Craig K. R. Willis
- Department of Biology and Centre for Forest Interdisciplinary Research (C-FIR); University of Winnipeg; Winnipeg MB Canada
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29
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Affiliation(s)
- Helen K. Pigage
- Biology Department, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado 80918, U.S.A. (e-mail: )
| | - Jon C. Pigage
- Biology Department, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado 80918, U.S.A. (e-mail: )
| | - John R. Demboski
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, Colorado 80025, U.S.A. (e-mail: )
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30
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Malaney JL, Demboski JR, Cook JA. Integrative species delimitation of the widespread North American jumping mice (Zapodinae). Mol Phylogenet Evol 2017; 114:137-152. [PMID: 28600183 DOI: 10.1016/j.ympev.2017.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023]
Abstract
Delimiting species can be challenging, but is a key step for the critical examination of evolutionary history and for prioritizing conservation efforts. Because systematic relationships are often determined iteratively using tests based on taxonomy, such methods can fail to detect cryptic variation and result in biased conclusions. Conversely, discovery-based approaches provide a powerful way to define operational taxonomic units and test species boundaries. We compare both approaches (taxonomy-based delimitation - TBD and discovery-based delimitation - DBD) within North American jumping mice (Zapodinae) using broad sampling, multilocus analyses, and ecological tests. This group diversified through the dynamic glacial-interglacial periods of the Quaternary and phylogeographic tests reveal 28 lineages that correspond poorly with current taxonomy (4 species, 32 nominal subspecies). However, neither the 4-species or 28-lineage hypotheses are optimal for species-level classification. Rather, information theoretic approaches (Bayes Factors) indicate a 15-species hypothesis is best for characterizing genetic variation in this group, with subsequent iterative pairwise ecological tests failing to confirm four species pairs. Taken together, evolutionary and ecological tests capture divergence among 11 putative species that, if upheld by additional tests, will lead to taxonomic revision and reevaluation of conservation plans.
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Affiliation(s)
- Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA; Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA.
| | - Joseph A Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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31
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Assis APA, Rossoni DM, Patton JL, Marroig G. Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias). Evolution 2016; 71:595-609. [PMID: 27917480 DOI: 10.1111/evo.13137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 01/03/2023]
Abstract
The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species' divergence.
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Affiliation(s)
- Ana Paula A Assis
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of Sao Paulo, Sao Paulo, 05508-900, Brazil
| | - Daniela M Rossoni
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of Sao Paulo, Sao Paulo, 05508-900, Brazil
| | - James L Patton
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, California, 94720
| | - Gabriel Marroig
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of Sao Paulo, Sao Paulo, 05508-900, Brazil
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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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Hertach T, Puissant S, Gogala M, Trilar T, Hagmann R, Baur H, Kunz G, Wade EJ, Loader SP, Simon C, Nagel P. Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative. PLoS One 2016; 11:e0165562. [PMID: 27851754 PMCID: PMC5112989 DOI: 10.1371/journal.pone.0165562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 11/23/2022] Open
Abstract
Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture.
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Affiliation(s)
- Thomas Hertach
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
- * E-mail:
| | - Stéphane Puissant
- Muséum–Jardin des Sciences, Mairie de Dijon, Dijon, France
- Institut de Systématique, Évolution, Biodiversité, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - Matija Gogala
- Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
| | - Tomi Trilar
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Reto Hagmann
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
| | - Hannes Baur
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
- University of Bern, Institute of Ecology and Evolution, Bern, Switzerland
| | - Gernot Kunz
- Department of Zoology, Karl Franzens University of Graz, Graz, Austria
| | - Elizabeth J. Wade
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- United States Department of Agriculture, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, Florida, United States of America
| | - Simon P. Loader
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Life Sciences Department, University of Roehampton, London, United Kingdom
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Peter Nagel
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
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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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Hoberg EP, Makarikov AA, Tkach VV, Meagher S, Nims TN, Eckerlin RP, Galbreath KE. Insights on the host associations and geographic distribution of Hymenolepis folkertsi (Cestoda: Hymenolepididae) among rodents across temperate latitudes of North America. Parasitol Res 2016; 115:4627-4638. [PMID: 27630100 PMCID: PMC5104796 DOI: 10.1007/s00436-016-5255-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/07/2016] [Indexed: 11/01/2022]
Abstract
Synoptic data and an understanding of helminth parasite diversity among diverse rodent assemblages across temperate latitudes of North America remain remarkably incomplete. Renewed attention to comprehensive survey and inventory to establish the structure of biodiverse faunas is essential in providing indicators and proxies for identifying the outcomes of accelerating change linked to climate warming and anthropogenic forcing. Subsequent to the description of Hymenolepis folkertsi in the oldfield mouse, Peromyscus polionotus, additional specimens of hymenolepidids were collected or discovered in archived museum repositories from multiple species of deer mice (Peromyscus maniculatus, Peromyscus leucopus), the golden mouse (Ochrotomys nuttalli), chipmunks (Tamias striatus, Tamias amoenus), the 13-lined ground squirrel (Ictidomys tridecemlineatus), and tree squirrels (Sciurus carolinensis, Sciurus niger) from disjunct localities in the USA spanning southern Georgia, Virginia, Pennsylvania, Connecticut, the Upper Peninsula of Michigan, Wisconsin, and central Idaho. Specimens were largely consistent morphologically with the original description of H. folkertsi. Initial DNA sequence data, from a portion of the mitochondrial NADH dehydrogenase subunit 1, demonstrated intraspecific variation among three apparently geographically isolated populations attributed to H. folkertsi (uncorrected genetic distances of 2.7 % (Idaho and Michigan), 2.4 % (Virginia + Pennsylvania and Michigan), and 1.89 % (VA + PA and ID). Geography rather than host association explains the distribution and occurrence of H. folkertsi, and host colonization among deer mice, chipmunks, and other sciurids within regional sites is indicated. Genetic divergence revealed across localities for H. folkertsi suggests historically isolated populations, consistent with extended evolutionary and biogeographic trajectories among hymenolepidids and species of Peromyscus and Tamias in North America. Field inventory, that revealed these parasite populations, substantially alters our understanding of the distribution of diversity and provides insights about the nature of the complex relationships that serve to determine cestode faunas in rodents.
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Affiliation(s)
- E P Hoberg
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Bldg 1180 BARC East, 10300, Baltimore Avenue, Beltsville, MD, USA.
| | - A A Makarikov
- Institute of Systematics and Ecology of Animals, Siberian Branch Russian Academy of Sciences, Frunze Str. 11, Novosibirsk, 630091, Russia
| | - V V Tkach
- Department of Biology, University of North Dakota, 10 Cornell Street, 58202, Grand Forks, ND, USA
| | - S Meagher
- Department of Biological Sciences, Western Illinois University, 61455, Macomb, IL, USA
| | - T N Nims
- Science Department, Perimeter College at Georgia State University, 239 Cedar Lane, 30014, Covington, GA, USA
| | - R P Eckerlin
- Mathematics, Science and Engineering Division, Northern Virginia Community College, 22003, Annandale, VA, USA
| | - K E Galbreath
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave., 49855, Marquette, MI, USA
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36
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Sun Y, Surget-Groba Y, Gao S. Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae). Mol Ecol 2016; 25:4580-92. [PMID: 27447352 DOI: 10.1111/mec.13764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 06/18/2016] [Accepted: 07/02/2016] [Indexed: 01/20/2023]
Abstract
Local adaptation to different environments has the potential to maintain divergence between populations despite recurrent gene flow and is an important driver for generating biological diversity. In this study, we investigate the role of adaptation in the maintenance of two parapatric varieties of a forest tree. We used sequence variation of chloroplastic DNA and restriction site-associated DNA to investigate the genetic structure of two varieties of Castanopsis carlesii in subtropical China and relate it to climatic variation. We used niche reconstruction methods to investigate niche differentiation between the two varieties and to estimate the past distribution of this species. A deep divergence was observed between the two varieties, but evidence of introgression and genetic admixture was detected in two phenotypically and geographically intermediate populations. Niche reconstruction suggests that the distribution of the two varieties was disjunct during periods of global cooling and that the two varieties occupy significantly different niches. The genetic structure was mainly driven by environmental factors, and 13 outlier loci under divergent selection were correlated with climatic variation. These results suggest that the two varieties evolved in allopatry and came back into secondary contact after the last glacial maximum and that they are an evolutionary example of divergence maintained by climatic selection despite recurrent gene flow.
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Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China. , .,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. ,
| | - Yann Surget-Groba
- Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, 58 rue Principale, Ripon, Quebec, J0V 1V0, Canada.,Quebec Centre for Biodiversity Science, McGill University, 1205 Dr. Penfield Avenue, Montreal, Quebec, H3A 1B1, Canada
| | - Shaoxiong Gao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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37
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McLean BS, Jackson DJ, Cook JA. Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels (Urocitellus). Mol Phylogenet Evol 2016; 102:174-88. [DOI: 10.1016/j.ympev.2016.05.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
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38
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Reifová R, Majerová V, Reif J, Ahola M, Lindholm A, Procházka P. Patterns of gene flow and selection across multiple species of Acrocephalus warblers: footprints of parallel selection on the Z chromosome. BMC Evol Biol 2016; 16:130. [PMID: 27311647 PMCID: PMC4910229 DOI: 10.1186/s12862-016-0692-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Background Understanding the mechanisms and selective forces leading to adaptive radiations and origin of biodiversity is a major goal of evolutionary biology. Acrocephalus warblers are small passerines that underwent an adaptive radiation in the last approximately 10 million years that gave rise to 37 extant species, many of which still hybridize in nature. Acrocephalus warblers have served as model organisms for a wide variety of ecological and behavioral studies, yet our knowledge of mechanisms and selective forces driving their radiation is limited. Here we studied patterns of interspecific gene flow and selection across three European Acrocephalus warblers to get a first insight into mechanisms of radiation of this avian group. Results We analyzed nucleotide variation at eight nuclear loci in three hybridizing Acrocephalus species with overlapping breeding ranges in Europe. Using an isolation-with-migration model for multiple populations, we found evidence for unidirectional gene flow from A. scirpaceus to A. palustris and from A. palustris to A. dumetorum. Gene flow was higher between genetically more closely related A. scirpaceus and A. palustris than between ecologically more similar A. palustris and A. dumetorum, suggesting that gradual accumulation of intrinsic barriers rather than divergent ecological selection are more efficient in restricting interspecific gene flow in Acrocephalus warblers. Although levels of genetic differentiation between different species pairs were in general not correlated, we found signatures of apparently independent instances of positive selection at the same two Z-linked loci in multiple species. Conclusions Our study brings the first evidence that gene flow occurred during Acrocephalus radiation and not only between sister species. Interspecific gene flow could thus be an important source of genetic variation in individual Acrocephalus species and could have accelerated adaptive evolution and speciation rate in this avian group by creating novel genetic combinations and new phenotypes. Independent instances of positive selection at the same loci in multiple species indicate an interesting possibility that the same loci might have contributed to reproductive isolation in several speciation events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0692-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
| | - Veronika Majerová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Markus Ahola
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Turku, Finland.,Natural Resources Institute Finland, Itäinen Pitkäkatu 3, FI-20240, Turku, Finland
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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39
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Hope AG, Malaney JL, Bell KC, Salazar-Miralles F, Chavez AS, Barber BR, Cook JA. Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests. Mol Phylogenet Evol 2016; 100:170-182. [PMID: 27083861 DOI: 10.1016/j.ympev.2016.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/27/2022]
Abstract
Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
| | - Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA.
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Fernando Salazar-Miralles
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
| | - Brian R Barber
- Biodiversity Institute, University of Wyoming, Laramie, WY 82071, USA.
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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40
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Mao X, Zhang S, Rossiter SJ. Differential introgression suggests candidate beneficial and barrier loci between two parapatric subspecies of Pearson's horseshoe bat Rhinolophus pearsoni. Curr Zool 2016; 62:405-412. [PMID: 29491929 PMCID: PMC5829442 DOI: 10.1093/cz/zow017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/05/2015] [Indexed: 11/13/2022] Open
Abstract
Observations that rates of introgression between taxa can vary across loci are
increasingly common. Here, we test for differential locus-wise introgression in 2
parapatric subspecies of Pearson′s horseshoe bat (Rhinolophus pearsoni
chinensis and R. p. pearsoni). To efficiently identify
putative speciation genes and/or beneficial genes in our current system, we used a
candidate gene approach by including loci from X chromosome that are suggested to be more
likely involved in reproductive isolation in other organisms and loci underlying hearing
that have been suggested to spread across the hybrid zone in another congeneric species.
Phylogenetic and coalescent analyses were performed at 2 X-linked, 4 hearing genes, as
well as 2 other autosomal loci individually. Likelihood ratio tests could not reject the
model of zero gene flow at 2 X-linked and 2 autosomal genes. In contrast, gene flow was
supported at 3 of 4 hearing genes. While this introgression could be adaptive, we cannot
rule out stochastic processes. Our results highlight the utility of the candidate gene
approach in searching for speciation genes and/or beneficial genes across the species
boundary in natural populations.
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Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China and.,School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Shuyi Zhang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China and
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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41
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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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42
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Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res 2016; 26:1-11. [PMID: 26518481 PMCID: PMC4691742 DOI: 10.1101/gr.186668.114] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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43
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Good JM, Vanderpool D, Keeble S, Bi K. Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks. Evolution 2015; 69:1961-72. [DOI: 10.1111/evo.12712] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 06/11/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Jeffrey M. Good
- Division of Biological Sciences; University of Montana; Missoula Montana 59812
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
| | - Dan Vanderpool
- Division of Biological Sciences; University of Montana; Missoula Montana 59812
| | - Sara Keeble
- Division of Biological Sciences; University of Montana; Missoula Montana 59812
| | - Ke Bi
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
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44
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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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