Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum

Stephanie Greaves, David Chapple, Charles Daugherty, Dianne Gleeson, Peter Ritchie

    Research output: Contribution to journalArticle

    29 Citations (Scopus)

    Abstract

    Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.
    Original languageEnglish
    Pages (from-to)853-864
    Number of pages12
    JournalJournal of Biogeography
    Volume35
    DOIs
    Publication statusPublished - 2008

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    Scincidae
    divergence
    Pleistocene
    genetic variation
    Bayesian theory
    cytochrome b
    haplotypes
    coasts
    phylogeny
    cytochrome
    Pliocene
    genes
    testing
    phylogenetics
    gene
    coast
    methodology
    method

    Cite this

    Greaves, Stephanie ; Chapple, David ; Daugherty, Charles ; Gleeson, Dianne ; Ritchie, Peter. / Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum. In: Journal of Biogeography. 2008 ; Vol. 35. pp. 853-864.
    @article{1f4832e1e37f4849afdfec1801957803,
    title = "Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum",
    abstract = "Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5{\%}. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.",
    keywords = "Cytochrome b, glacial refugia, historical biogeography, lizard, mtDNA, ND2, ND4, New Zealand, phylogeography, Pliocene divergence.",
    author = "Stephanie Greaves and David Chapple and Charles Daugherty and Dianne Gleeson and Peter Ritchie",
    year = "2008",
    doi = "10.1111/j.1365-2699.2007.01848.x",
    language = "English",
    volume = "35",
    pages = "853--864",
    journal = "Journal of Biogeography",
    issn = "0305-0270",
    publisher = "Wiley-Blackwell",

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    Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum. / Greaves, Stephanie; Chapple, David; Daugherty, Charles; Gleeson, Dianne; Ritchie, Peter.

    In: Journal of Biogeography, Vol. 35, 2008, p. 853-864.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum

    AU - Greaves, Stephanie

    AU - Chapple, David

    AU - Daugherty, Charles

    AU - Gleeson, Dianne

    AU - Ritchie, Peter

    PY - 2008

    Y1 - 2008

    N2 - Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.

    AB - Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.

    KW - Cytochrome b

    KW - glacial refugia

    KW - historical biogeography

    KW - lizard

    KW - mtDNA

    KW - ND2

    KW - ND4

    KW - New Zealand

    KW - phylogeography

    KW - Pliocene divergence.

    U2 - 10.1111/j.1365-2699.2007.01848.x

    DO - 10.1111/j.1365-2699.2007.01848.x

    M3 - Article

    VL - 35

    SP - 853

    EP - 864

    JO - Journal of Biogeography

    JF - Journal of Biogeography

    SN - 0305-0270

    ER -