Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

BACKGROUND: Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. CONCLUSIONS/SIGNIFICANCE: Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species

The origins of the enigmatic Falkland Islands wolf

Extent: 7p.The origin of the extinct Falkland Island wolf (FIW), Dusicyon australis, has remained a mystery since it was first recorded by Europeans in the 17th Century. It is the only terrestrial mammal on the Falkland Islands (also known as the Malvinas Islands) which lie ~460km from Argentina, leading to suggestions of either human-mediated transport or over-water dispersal. Previous studies used ancient DNA from museum specimens to suggest that the FIW diverged from its closest living relative, the South American maned wolf (Chrysocyon brachyurus) around 7 Ma, and colonized the islands ~330 ka by unknown means. In contrast, we retrieve ancient DNA from subfossils of an extinct mainland relative, Dusicyon avus, and reveal the FIW lineage became isolated only 16 ka (8-31 ka), during the last glacial phase. Submarine terraces, formed on the Argentine coastal shelf by low sea-stands during this period, suggest that the FIW colonized via a narrow, shallow marine strait, potentially while it was frozen over.Jeremy J. Austin, Julien Soubrier, Francisco J. Prevosti, Luciano Prates, Valentina Trejo, Francisco Mena & Alan Coope

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Funder: The excavation of the Ikawazu Jomon individual was supported by Grant-in-Aid for Scientific Research (B) (25284157) to YY. The Ikawazu Jomon genome project was organized by HI, and TH & HO who were supported by MEXT KAKENHI Grant Numbers 16H06408 and 17H05132, by Grant-in-Aid for Scientific Research on Innovative Areas (Cultural History of Paleoasia), and by Grant-in-Aid for Challenging Exploratory Research (23657167) and for Scientific Research (B) (17H03738). The Ikawazu Jomon genome sequencing was supported by JSPS KAKENHI Grant Number 16H06279 to ATo, and partly supported in the CHOZEN project in Kanazawa University, and in the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University. Computations for the Ikawazu Jomon genome were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.Abstract: Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia

Ancient plant DNA in archaeobotany

Holozän - aDNA - Archäobotanik - Makroreste - Genetik - Getreide - Früchte - Holz - Methode - Kulturpflanzen - Vegetationsgeschichte - Ernährun