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Jack Sullivan - One of the best experts on this subject based on the ideXlab platform.

  • Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes
    Systematic biology, 2011
    Co-Authors: Noah M. Reid, John R. Demboski, Jack Sullivan
    Abstract:

    The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: NeoTamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion. (Coalescent simulation; gene tree; hybridization; introgression; lineage sorting; multilocus; reproductive proteins; Sciuridae; species tree; Tamias.)

  • extensive mtdna variation within the yellow pine chipmunk Tamias amoenus rodentia sciuridae and phylogeographic inferences for northwest north america
    Molecular Phylogenetics and Evolution, 2003
    Co-Authors: John R. Demboski, Jack Sullivan
    Abstract:

    Abstract The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.

  • Phylogeography and introgressive hybridization : chipmunks (Genus Tamias) in the northern rocky mountains
    Evolution; international journal of organic evolution, 2003
    Co-Authors: Jeffrey M. Good, John R. Demboski, David W. Nagorsen, Jack Sullivan
    Abstract:

    If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical frame- work is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudusand Tamias amoenus, in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across mor- phologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias. Our results illustrate the utility of phylogeographic analyses for detecting in- stances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.

Jeanlouis Chapuis - One of the best experts on this subject based on the ideXlab platform.

  • Borréliose de Lyme : situation générale et conséquences de l’introduction en Île-de-France d’un nouvel hôte, le tamia de Sibérie
    Bulletin Epidémiologique Hebdomadaire - BEH, 2010
    Co-Authors: Jeanlouis Chapuis, Elisabeth Ferquel, Olivier Patey, Gwenaël Vourc'h, Muriel Cornet
    Abstract:

    L’épidémiologie de la borréliose de Lyme demeure encore peu connue en France, les données étant très parcellaires. Les études d’incidence ont mon- tré une grande disparité entre les régions, avec des niveaux de risque éle- vés en Alsace, Lorraine, Limousin, Auvergne et Rhône-Alpes. Les études vectorielles associées montrent des corrélations entre incidences et densi- tés en nymphes infectées, mais les exceptions sont fréquentes. Dans des forêts d’Île-de-France et de Picardie, l’introduction du tamia de Sibérie pourrait intervenir dans la dynamique de la borréliose de Lyme. Cet écureuil semble en effet être réservoir de cette maladie, il porte de fortes charges en Ixodes ricinus et, de plus, il montre une tolérance accrue vis-à-vis des espèces de Borrelia, comparativement aux autres réservoirs. Les recherches en cours visent à préciser le rôle de cet écureuil exotique dans l’incidence de cette maladie en périphérie de la Forêt de Sénart (Essonne) où la popu- lation de Tamias est estimée entre 10 000 et 20 000 individus.

  • Helminth fauna of the Siberian chipmunk, Tamias sibiricus Laxmann (Rodentia, Sciuridae) introduced in suburban French forests
    Parasitology Research, 2007
    Co-Authors: Benoît Pisanu, Julie Marmet, Christelle Jerusalem, Cindy Huchery, Jeanlouis Chapuis
    Abstract:

    The spread of an immigrant host species can be influenced both by its specific helminth parasites that come along with it and by newly acquired infections from native fauna. The Siberian chipmunk, Tamias sibiricus Laxmann (Rodentia, Sciuridae), a northeastern Eurasiatic ground nesting Sciurid, has been introduced in France for less than three decades. Thirty individuals were collected from three suburban forests in the Ile-de-France Region between 2002 and 2006. Two intestinal nematode species dominated the helminth fauna: Brevistriata skrjabini [Prevalence, P , 99% C.I., 87% (64–97%); mean intensity, M.I., 99% C.I., 43 (28–78)] and Aonchotheca annulosa [ P , 47% (25–69%); M.I., 35 (3–157)]. B. skrjabini is a direct life cycle nematode species of North Eurasiatic origin, with a restricted spectrum of phylogenetically related suitable hosts. This result indicates that B. skrjabini successfully settled and spread with founder pet chipmunks maintained in captivity and released in natura . Chipmunks acquired A. annulosa , a nematode species with a large spectrum of phylogenetically unrelated suitable host species, from local Muroid rodent species with similar behavior, life-history traits and habitats. Quantitative studies are needed to evaluate the potential for both B. skrjabini and A. annulosa to impede the spread of Tamias and for B. skrjabini to favor chipmunk colonization through detrimental effects upon native co-inhabiting host species.

  • repartition en france d un animal de compagnie naturalise le tamia de siberie Tamias sibiricus
    Revue d'écologie, 2005
    Co-Authors: Jeanlouis Chapuis
    Abstract:

    Apparu dans les animaleries de differents pays europeens au cours des annees 1960, le Tamia de Siberie (Tamias sibiricus), Sciuride originaire d'Asie, a ete lâche dans la nature a la fin des annees 1970. Une enquete nationale lancee en 2000 aupres des agents de l'Office National des Forets, completee par diverses autres informations, a permis de recenser sept populations implantees dans des forets periurbaines et des parcs urbains de la Region Ile-de-France, et trois populations dans des forets de la Region Picardie. Certaines de ces populations comptent actuellement plusieurs milliers d'individus. Leur presence est liee a l'introduction deliberee d'un nombre inconnu, mais probablement reduit dans chaque cas, d'individus dont la compagnie lassait leurs proprietaires. Seule la population situee a Villers-Carbonnel (Picardie) provient d'une trentaine de lamias echappes d'un elevage. Sur certains sites, la vitesse de colonisation est comprise entre 200 et 250 m par an au cours des premieres decennies ayant suivi l'introduction. La population de la foret de Meudon (Hauts-de-Seine) a fait l'objet de denombrements hebdomadaires, sur itineraire-echantillon, de mars 2000 a fevrier 2004. En 2002, 15 adultes marques avec une bague auriculaire identifiable a distance ont ete suivis d'avril a octobre. Ces observations et celles provenant de travaux effectues sur son aire d'origine, dans d'autres pays europeens ou en captivite, permettent de cerner ses principaux traits d'histoire de vie et de disposer d'elements permettant d'analyser sa propension a devenir une espece envahissante en France.

Janet E. Foley - One of the best experts on this subject based on the ideXlab platform.

Mary H. Straub - One of the best experts on this subject based on the ideXlab platform.

John R. Demboski - One of the best experts on this subject based on the ideXlab platform.

  • Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes
    Systematic biology, 2011
    Co-Authors: Noah M. Reid, John R. Demboski, Jack Sullivan
    Abstract:

    The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: NeoTamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion. (Coalescent simulation; gene tree; hybridization; introgression; lineage sorting; multilocus; reproductive proteins; Sciuridae; species tree; Tamias.)

  • extensive mtdna variation within the yellow pine chipmunk Tamias amoenus rodentia sciuridae and phylogeographic inferences for northwest north america
    Molecular Phylogenetics and Evolution, 2003
    Co-Authors: John R. Demboski, Jack Sullivan
    Abstract:

    Abstract The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.

  • Phylogeography and introgressive hybridization : chipmunks (Genus Tamias) in the northern rocky mountains
    Evolution; international journal of organic evolution, 2003
    Co-Authors: Jeffrey M. Good, John R. Demboski, David W. Nagorsen, Jack Sullivan
    Abstract:

    If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical frame- work is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudusand Tamias amoenus, in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across mor- phologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias. Our results illustrate the utility of phylogeographic analyses for detecting in- stances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.

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