Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus

Tex, Robert-Jan den; Thorington, Richard W.; Maldonado, Jesús E.; Leonard, Jennifer A.

doi:10.1016/j.ympev.2009.12.023

Cited by 49 publications

(46 citation statements)

References 38 publications

(48 reference statements)

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“…Phylogenetic patterns and molecular dating in squirrels ( Sundasciurus ) indicated an old (Miocene or Pliocene) origin of montane clades and subsequent (Pliocene) diversification among montane regions (den Tex et al, 2010), and thus no influence from Pleistocene sea level and habitat changes. Barbets ( Megalaima ) display a different pattern, with montane endemics from each island related to widespread lowland species, rather than other montane taxa (den Tex & Leonard, 2013).…”

Section: Discussionmentioning

confidence: 99%

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Moyle

Manthey

Hosner

et al. 2017

PeerJ

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Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.

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Section: Discussionmentioning

confidence: 99%

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Moyle

Manthey

Hosner

et al. 2017

PeerJ

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“…These results highlight the need to be aware of the possibility of numts even in degraded or ancient material, but also suggest that the inclusion of nuclear markers in some studies based on degraded and/or historic material may be more feasible Leonard et al (2005) or by DNeasy animal tissue and blood extraction kit (Qiagen, Hilden, Germany) following the animal tissue protocol as in Den Tex et al (2010). To monitor for contamination, negative extractions were included in every batch of extractions.…”

Section: Introductionmentioning

confidence: 99%

“…To monitor for contamination, negative extractions were included in every batch of extractions. The whole cob gene region was amplified from muscle tissue samples in a single amplification in order to minimize the risk of amplifying nuclear copies, and used as a reference to design more squirrel specific primers for use in the museum material (den Tex et al 2010). Historic squirrel specimens were amplified using 52 different primer sets, some of which were mammal ''universal'' (n = 23), and some of which were designed for these squirrels, and will be referred to here as ''specific'' primer sets (n = 29).…”

Section: Introductionmentioning

confidence: 99%

Nuclear copies of mitochondrial genes: another problem for ancient DNA

et al. 2010

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The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.R.-J. den Tex · J. A. Leonard (&)

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“…First, paleo-climatic and vegetation modeling must address geologic events earlier than the LGM. Based on genetic divergence values in a wide variety of studies in addition to our own (e.g., Gorog et al 2004, den Tex et al 2010, Ohtani et al 2013, the timescale of Borneo's avifaunal division is two orders of magnitude older than the LGM, perhaps nearer one million years than 10,000 years. Thus, models explaining the state of geography at the LGM, although extremely helpful in indicating what may happen to habitats during glacial cycles, may not apply to the mid or early Pleistocene.…”

Section: Black-eye Phylogeography and Bornean Bird Diversificationmentioning

confidence: 93%

Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae)

Gawin

Rahman

Ramji

et al. 2014

The Auk

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The Mountain Black-eye (Chlorocharis emiliae) is an endemic white-eye (Zosteropidae) of Borneo with a unique ''sky island'' distribution. We compared mitochondrial ND2, ND3, Cytb, and control region DNA sequences (2,194 nucleotides) to study the phylogeographic relationships of five populations of this species that span its range: Mounts Kinabalu, Trus Madi, Murud, Mulu, and Pueh. These comparisons showed that black-eyes are divided into two main clades that correspond generally to subspecific morphological groups: one in Sabah, Malaysia (Kinabalu and Trus Madi), and one in Sarawak, Malaysia (Murud, Mulu, and Pueh). The genetic and morphologic subdivision of black-eyes disputes the expected merging of populations during the Last Glacial Maximum (LGM), when montane forest presumably expanded and provided the opportunity for currently isolated populations to intermingle. Instead the genetic aging of black-eye populations indicates they diversified long before the LGM, and either did not expand sufficiently in range during the LGM to reach one another, or were reproductively isolated by the time of the LGM and thus prevented from interbreeding. Moreover, the subdivision between black-eyes in Sabah and Sarawak means that this species (and probably several other montane species) has a phylogeographic structure remarkably similar to Borneo's lowland bird populations, which are presumed to have evolved under different paleo-geographic conditions. The similar phylogeographic pattern found in both montane and lowland species requires that we rethink the causes of bird population diversification on the island of Borneo. Keywords: Greater Sunda Islands, last glacial maximum, montane avifauna, phylogeography, refugia, sky islands, ZosteropidaePatrons de diversification aviaireà Bornéo: Le cas d'une espèce endémique, Chlorocharis emiliae RÉSUMÉ Chlorocharis emiliae est une espèce endémique de Zosteropidae de Bornéo ayant une répartition unique de type ''sky island.'' Nous avons comparé les séquences d'ADN mitochondrial ND2, ND3, Cytb, et de la région de contrôle (2,194 nucléotides) afin d'étudier les relations phylogéographiques de cinq populations de cette espèce qui couvrent toute son aire de répartition: Les Monts Kinabalu, Trus Madi, Murud, Mulu, et Pueh. Ces comparaisons ont montré que C. emiliae se divise en deux principaux clades qui correspondent généralement aux groupes morphologiques sousspécifiques: unà Sabah, en Malaisie (Kinabalu et Trus Madi) et unà Sarawak, en Malaisie (Murud, Mulu, et Pueh). La subdivision génétique et morphologique de C. emiliae conteste l'hypothèse de fusion des populations au cours du dernier maximum glaciaire (DMG), lorsque la forêt montagnarde s'est vraisemblablement développée et a fourni aux populations actuellement isolées l'occasion de se mélanger. Au lieu de cela, le vieillissement génétique des populations de C. emiliae indique qu'elles se sont diversifiées bien avant le DMG, et que leur aire de répartition ne s'est pas suffisammentélargie au cours du DMG pour se rejoindr...

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Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus

Cited by 49 publications

References 38 publications

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Nuclear copies of mitochondrial genes: another problem for ancient DNA

Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae)

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