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

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

<p>Abstract</p> <p>Background</p> <p>Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera.</p> <p>Results</p> <p>Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing <it>Piliocolobus/Procolobus </it>and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from <it>Piliocolobus</it>/<it>Procolobus </it>into <it>Colobus</it>. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, <it>Semnopithecus </it>diverged first, indicating langur paraphyly. However, unidirectional gene flow from <it>Semnopithecus </it>into <it>Trachypithecus </it>via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene.</p> <p>Conclusions</p> <p>Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.</p

Evolutionary History of the Odd-Nosed Monkeys and the Phylogenetic Position of the Newly Described Myanmar Snub-Nosed Monkey Rhinopithecus strykeri

Odd-nosed monkeys represent one of the two major groups of Asian colobines. Our knowledge about this primate group is still limited as it is highlighted by the recent discovery of a new species in Northern Myanmar. Although a common origin of the group is now widely accepted, the phylogenetic relationships among its genera and species, and the biogeographic processes leading to their current distribution are largely unknown. To address these issues, we have analyzed complete mitochondrial genomes and 12 nuclear loci, including one X chromosomal, six Y chromosomal and five autosomal loci, from all ten odd-nosed monkey species. The gene tree topologies and divergence age estimates derived from different markers were highly similar, but differed in placing various species or haplogroups within the genera Rhinopithecus and Pygathrix. Based on our data, Rhinopithecus represent the most basal lineage, and Nasalis and Simias form closely related sister taxa, suggesting a Northern origin of odd-nosed monkeys and a later invasion into Indochina and Sundaland. According to our divergence age estimates, the lineages leading to the genera Rhinopithecus, Pygathrix and Nasalis+Simias originated in the late Miocene, while differentiation events within these genera and also the split between Nasalis and Simias occurred in the Pleistocene. Observed gene tree discordances between mitochondrial and nuclear datasets, and paraphylies in the mitochondrial dataset for some species of the genera Rhinopithecus and Pygathrix suggest secondary gene flow after the taxa initially diverged. Most likely such events were triggered by dramatic changes in geology and climate within the region. Overall, our study provides the most comprehensive view on odd-nosed monkey evolution and emphasizes that data from differentially inherited markers are crucial to better understand evolutionary relationships and to trace secondary gene flow

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution

The Lake CHAd Deep DRILLing project (CHADRILL) - targeting ~ 10 million years of environmental and climate change in Africa

At present, Lake Chad ( ~13°0 N, ~14° E) is a shallow freshwater lake located in the Sahel/Sahara region of central northern Africa. The lake is primarily fed by the Chari-Logone river system draining a ~600 000 km2 watershed in tropical Africa. Discharge is strongly controlled by the annual passage of the intertropical convergence zone (ITCZ) and monsoon circulation leading to a peak in rainfall during boreal summer. During recent decades, a large number of studies have been carried out in the Lake Chad Basin (LCB). They have mostly focused on a patchwork of exposed lake sediments and outcrops once inhabited by early hominids. A dataset generated from a 673m long geotechnical borehole drilled in 1973, along with outcrop and seismic reflection studies, reveal several hundred metres of Miocene-Pleistocene lacustrine deposits. CHADRILL aims to recover a sedimentary core spanning the Miocene-Pleistocene sediment succession of Lake Chad through deep drilling. This record will provide significant insights into the modulation of orbitally forced changes in northern African hydroclimate under different climate boundary conditions such as high CO2 and absence of Northern Hemisphere ice sheets. These investigations will also help unravel both the age and the origin of the lake and its current desert surrounding. The LCB is very rich in early hominid fossils (Australopithecus bahrelghazali; Sahelanthropus tchadensis) of Late Miocene age. Thus, retrieving a sediment core from this basin will provide the most continuous climatic and environmental record with which to compare hominid migrations across northern Africa and has major implications for understanding human evolution. Furthermore, due to its dramatic and episodically changing water levels and associated depositional modes, Lake Chad's sediments resemble maybe an analogue for lake systems that were once present on Mars. Consequently, the study of the subsurface biosphere contained in these sediments has the potential to shed light on microbial biodiversity present in this type of depositional environment. We propose to drill a total of ~1800m of poorly to semi-consolidated lacustrine, fluvial, and eolian sediments down to bedrock at a single on-shore site close to the shoreline of present-day Lake Chad. We propose to locate our drilling operations on-shore close to the site where the geotechnical Bol borehole (13°280 N, 14°440 E) was drilled in 1973. This is for two main reasons: (1) nowhere else in the Chad Basin do we have such detailed information about the lithologies to be drilled; and (2) the Bol site is close to the depocentre of the Chad Basin and therefore likely to provide the stratigraphically most continuous sequence

New infant cranium from the African Miocene sheds light on ape evolution

The evolutionary history of extant hominoids (humans and apes) remains poorly understood. The African fossil record during the crucial time period, the Miocene epoch, largely comprises isolated jaws and teeth, and little is known about ape cranial evolution. Here we report on the, to our knowledge, most complete fossil ape cranium yet described, recovered from the 13 million-year-old Middle Miocene site of Napudet, Kenya. The infant specimen, KNM-NP 59050, is assigned to a new species of Nyanzapithecus on the basis of its unerupted permanent teeth, visualized by synchrotron imaging. Its ear canal has a fully ossified tubular ectotympanic, a derived feature linking the species with crown catarrhines. Although it resembles some hylobatids in aspects of its morphology and dental development, it possesses no definitive hylobatid synapomorphies. The combined evidence suggests that nyanzapithecines were stem hominoids close to the origin of extant apes, and that hylobatid-like facial features evolved multiple times during catarrhine evolution

Stratigraphic, sedimentological and paleomagnetic study of the Kocabas travertines, Denizli Basin, Anatolia, Turkey, bearing Quaternary fossil remains

Stratigraphic, sedimentological and paleomagnetic studies were conducted on the travertine from Denizli Basin, near Kocabas village, in the Denizli region in Turkey, following the paleontological discovery in 2002. The stratigraphic and sedimentological studies show at least two main cycles of mass travertine, separated by a fluvial deposit and overlain by a fluvio-lacustrine deposit. These travertines must have formed in environments with strong hydrodynamics (streams or waterfalls) and are preferentially located at breaks of slopes. The paleomagnetic study shows that all the quarry travertine presents reverse magnetic polarity. On the other hand, the detrital fluvio-lacustrine deposit above the travertine presents normal geomagnetic polarity, except at the top, where it is reversed. Given the presence of an archaic Homo erectus skull and Villafranchian paleontological remains in the upper travertine unit, the whole travertine dates from the upper Matuyama, and is more recent than the Olduvai event (1.78 Ma). The normal polarity recorded in the upper fluvio-lacustrine deposit could correspond to the Cobb Mountain excursion, dated to 1.22 Ma. (C) 2014 Elsevier Masson SAS. All rights reserved

Stratigraphic, sedimentological and paleomagnetic study of the Kocabas travertines, Denizli Basin, Anatolia, Turkey, bearing Quaternary fossil remains

Stratigraphic, sedimentological and paleomagnetic studies were conducted on the travertine from Denizli Basin, near Kocabas village, in the Denizli region in Turkey, following the paleontological discovery in 2002. The stratigraphic and sedimentological studies show at least two main cycles of mass travertine, separated by a fluvial deposit and overlain by a fluvio-lacustrine deposit. These travertines must have formed in environments with strong hydrodynamics (streams or waterfalls) and are preferentially located at breaks of slopes. The paleomagnetic study shows that all the quarry travertine presents reverse magnetic polarity. On the other hand, the detrital fluvio-lacustrine deposit above the travertine presents normal geomagnetic polarity, except at the top, where it is reversed. Given the presence of an archaic Homo erectus skull and Villafranchian paleontological remains in the upper travertine unit, the whole travertine dates from the upper Matuyama, and is more recent than the Olduvai event (1.78 Ma). The normal polarity recorded in the upper fluvio-lacustrine deposit could correspond to the Cobb Mountain excursion, dated to 1.22 Ma. (C) 2014 Elsevier Masson SAS. All rights reserved

Turkey) at at least 1.1 Ma

Since its discovery within a travertine quarry, the fragmentary cranium of the only known Turkish Homo erectus, the Kocabas hominid, has led to conflicting biochronological estimations. First estimated to be similar to 500 lea old, the partial skull presents a combination of archaic and evolved features that puts it as an intermediate specimen between the Drnanisi fossils (Homo georgicus) and the Chinese Zhoukoudian skulls (Homo erectus) respectively dated to 1.8 to similar to 0.8 Ma. Here we present a multidisciplinary study combining sedimentological, paleontological and paleoanthropological observations together with cosmogenic nuclide concentration and paleomagnetic measurements to provide an absolute chronological framework for the Upper fossiliferous Travertine unit where the Kocabas hominid and fauna were discovered. The Al-26/(10) Be burial ages determined on pebbles from conglomeratic levels framing the Upper fossiliferous Travertine unit, which exhibits an inverse polarity, constrains its deposition to before the Cobb Mountain sub-chron, that is between 1.22 and similar to 1.5 Ma. The alternative match of the normal polarity recorded above the travertine with the Jaramillo subchron (lower limit 1.07 Ma) may also be marginally compatible with cosmogenic nuclides interpretation, thus the proposed minimum age of 1.1 Ma for the end of massive travertine deposition. The actual age of the fossils is likely to be in the 1.1-1.3 Ma range. This absolute date is in close agreement with the paleoanthropological conclusions based on morphometric comparisons implying that Kocabas hominid belongs to the Homo erectus s.l. group that includes Chinese and African fossils, and is different from Middle and Upper Pleistocene specimens. Furthermore, this date is confirmed by the large mammal assemblage, typical of the late Villafranchian. Because it attests to the antiquity of human occupation of the Anatolian Peninsula and one of the waves of settlements out of Africa, this work challenges the current knowledge of the Homo erectus dispersal over Eurasia. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/)