New evidence of megafaunal bone damage indicates late colonization of Madagascar

Copyright: © 2018 Anderson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The estimated period in which human colonization of Madagascar began has expanded recently to 5000–1000 y B.P., six times its range in 1990, prompting revised thinking about early migration sources, routes, maritime capability and environmental changes. Cited evidence of colonization age includes anthropogenic palaeoecological data 2500–2000 y B.P., megafaunal butchery marks 4200–1900 y B.P. and OSL dating to 4400 y B.P. of the Lakaton’i Anja occupation site. Using large samples of newly-excavated bone from sites in which megafaunal butchery was earlier dated >2000 y B.P. we find no butchery marks until ~1200 y B.P., with associated sedimentary and palynological data of initial human impact about the same time. Close analysis of the Lakaton’i Anja chronology suggests the site dates <1500 y B.P. Diverse evidence from bone damage, palaeoecology, genomic and linguistic history, archaeology, introduced biota and seafaring capability indicate initial human colonization of Madagascar 1350–1100 y B.P

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

<p>Abstract</p> <p>Background</p> <p>The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments.</p> <p>Results</p> <p>In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (<it>Coelodonta antiquitatis</it>), and the threatened Javan (<it>Rhinoceros sondaicus</it>), Sumatran (<it>Dicerorhinus sumatrensis</it>), and black (<it>Diceros bicornis</it>) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (<it>Ceratotherium simum</it>) and Indian (<it>Rhinoceros unicornis</it>) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse <it>vs </it>tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths.</p> <p>Conclusion</p> <p>Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies.</p> <p><it>"The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945)</it></p

Locating specimens of extinct tiger (Panthera tigris) subspecies: Javan tiger (P.t. sondaica), Balinese tiger (P.t. balica), and Caspian tiger (P.t. virgata), including previously unpublished specimens

Recent advances in multivariate statistics, and in ancient DNA techniques, have greatly increased understanding of tiger phylogeography. However, regardless of advances in analytical methodology, researchers will continue to need access to specimens for morphological measurements and sampling for genetic analysis. The tiger has become increasingly endangered, and out of the nine putative tiger subspecies, three (Javan, Balinese, and Caspian) have become extinct in the last 100 years, leaving the specimens kept in natural history collections as the only materials available for research. Frustratingly little information is widely available concerning the specimens of these extinct tiger subspecies. We conducted an extensive search for specimens of extinct tiger subspecies, and also developed a simple on-site method to assign unprovenanced and probable Indonesian specimens to either Javan/Balinese or Sumatran subspecies. We located a total of 88 Javan, 11 Balinese, and 46 Caspian tigers, including seven new Javan tigers, and three Balinese tigers that were not widely known previously. These specimens are critical for research in order to understand the intraspecific phylogeny and evolutionary history of the tiger