Journal ArticleDOI
The other side of the Sahulian coin: biogeography and evolution of Melanesian forest dragons (Agamidae)
Oliver J.S. Tallowin,Shai Meiri,Shai Meiri,Stephen C. Donnellan,Stephen Richards,Christopher C. Austin,Paul M. Oliver,Paul M. Oliver +7 more
TLDR
P patterns of lineage distribution and diversity suggest that extinction in Australia, and colonization and radiation on proto-Papuan islands, have both shaped the extant diversity and distribution of forest dragons since the mid-Miocene.Abstract:
\n New Guinea has been considered both as a refuge for mesic rainforest-associated lineages that contracted in response to the late Cenozoic aridification of Australia and as a centre of biotic diversification and radiation since the mid-Miocene or earlier. Here, we estimate the diversity and a phylogeny for the Australo-Papuan forest dragons (Sauria: Agamidae; ~20 species) in order to examine the following: (1) whether New Guinea and/or proto-Papuan Islands may have been a biogeographical refuge or a source for diversity in Australia; (2) whether mesic rainforest environments are ancestral to the entire radiation, as may be predicted by the New Guinea refuge hypothesis; and (3) more broadly, how agamid ecological diversity varies across the contrasting environments of Australia and New Guinea. Patterns of lineage distribution and diversity suggest that extinction in Australia, and colonization and radiation on proto-Papuan islands, have both shaped the extant diversity and distribution of forest dragons since the mid-Miocene. The ancestral biome for all Australo-Papuan agamids is ambiguous. Both rainforest and arid-adapted radiations probably started in the early Miocene. However, despite deep-lineage diversity in New Guinea rainforest habitats, overall species and ecological diversity is low when compared with more arid areas, with terrestrial taxa being strikingly absent.read more
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Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae).
Alex Slavenko,Karin Tamar,Oliver J.S. Tallowin,Allen Allison,Fred Kraus,Salvador Carranza,Shai Meiri +6 more
TL;DR: Papuascincus is a genus of skinks endemic to New Guinea's mountain regions, comprising two wide-ranging species and two species known only from their type series as discussed by the authors.
Journal ArticleDOI
New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline
Emmanuel F. A. Toussaint,Lloyd T. White,Helena Shaverdo,Athena Lam,Athena Lam,Suriani Surbakti,Rawati Panjaitan,Bob Sumoked,Thomas von Rintelen,Katayo Sagata,Michael Balke +10 more
TL;DR: In this paper, the authors used geospatial analysis techniques to compare their phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species.
Journal ArticleDOI
Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.
Daniel J. D. Natusch,Damien Esquerré,Jessica A. Lyons,Amir Hamidy,Alan R. Lemmon,Emily Moriarty Lemmon,Awal Riyanto,J. Scott Keogh,Stephen C. Donnellan +8 more
TL;DR: It is found that L. albertisii and L. meridionalis are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range.
Journal ArticleDOI
Disparate origins for endemic bird taxa from the ‘Gondwana Rainforests’ of Central Eastern Australia
TL;DR: The disparate divergence ages recovered among all eight taxa are consistent with the biota of the Central Eastern Australian Rainforests comprising isolates either of younger age and tropical lowland origins or of older age and temperate upland origins.
Journal ArticleDOI
A novel dataset to identify the endemic herpetofauna of the New Caledonia biodiversity hotspot with DNA barcodes
Justin M. Bernstein,Justin M. Bernstein,Todd R. Jackman,Ross A. Sadlier,Yun-yu Wang,Aaron M. Bauer +5 more
TL;DR: A near-complete DNA barcode dataset for New Caledonian lizards is generated, consisting of 601 mitochondrial CO1 sequences of 100 of the 107 described lizards, and a number of yet undescribed species, to assess the performance of CO1 in delimiting species recognised by other, more extensive data and in recovering phylogenetic signal.
References
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies
TL;DR: It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.