ORCID Profile
0000-0002-6144-4743
Current Organisation
University of Zurich
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Publisher: Oxford University Press (OUP)
Date: 16-10-2012
Abstract: A multitude of factors influence how natural populations are genetically structured, including dispersal barriers, inhomogeneous habitats, and social organization. Such population sub ision is of special concern in endangered species, as it may lead to reduced adaptive potential and inbreeding in local subpopulations, thus increasing the risk of future extinctions. With only 6600 animals left in the wild, Sumatran orangutans (Pongo abelii) are among the most endangered, but also most enigmatic, great ape species. In order to infer the fine-scale population structure and connectivity of Sumatran orangutans, we analyzed the most comprehensive set of s les to date, including mitochondrial hyper-variable region I haplotypes for 123 in iduals and genotypes of 27 autosomal microsatellite markers for 109 in iduals. For both mitochondrial and autosomal markers, we found a pronounced population structure, caused by major rivers, mountain ridges, and the Toba caldera. We found that genetic ersity and corresponding long-term effective population size estimates vary strongly among s ling regions for mitochondrial DNA, but show remarkable similarity for autosomal markers, hinting at male-driven long-distance gene flow. In support of this, we identified several in iduals that were most likely sired by males originating from other genetic clusters. Our results highlight the effect of natural barriers in shaping the genetic structure of great ape populations, but also point toward important dispersal corridors on northern Sumatra that allow for genetic exchange.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Wiley
Date: 30-03-2012
Publisher: Public Library of Science (PLoS)
Date: 07-05-2012
Publisher: Public Library of Science (PLoS)
Date: 15-11-2012
Publisher: Springer Science and Business Media LLC
Date: 25-07-2010
Publisher: Public Library of Science (PLoS)
Date: 30-07-2018
Publisher: Springer Science and Business Media LLC
Date: 03-2012
Publisher: Cold Spring Harbor Laboratory
Date: 09-02-2023
DOI: 10.1101/2023.02.08.526988
Abstract: The treponemal diseases yaws, bejel and syphilis, all caused by subspecies of the bacterium Treponema pallidum , are re-emerging worldwide, yet their origins and spread remain largely unresolved. Albeit still rare, reconstructed ancient genomes of various T. pallidum strains now exist, to complement the analyses on the modern-day ersity of treponemes. Here, we report a new high-coverage (35X) ancient genome of a historical T. pallidum subsp. pallidum strain from the 17th century. This novel addition, combined with a selection of 76 modern and historical strains, enables a new level of in-depth investigation of treponemal evolution across all humaninfecting strains, with detailed analyses on recombination, positive selection, and ergence history of T. pallidum subspecies. Altogether 18 recombinant genes with strong evidence for effects of positive selection are identified, potentially responsible for virulence and immune evasion. The profound impact of recombination is in particular demonstrated in the ersification of the yaws- and bejel-causing clades, as excluding these recombinant genes from phylogenetic analysis causes these well-separated subspecies to cluster into a single clade. Both the involvement of ancient genomes in several recombination events, and the molecular clock dating of the subspecies’ ergence history emphasize the importance of recombination in the early adaptations of all T. pallidum strains. These findings are crucial in resolving the evolutionary history of T. pallidum , and in understanding the functionalities of treponemes beyond what could be achieved with modern genomic data alone.
Publisher: Oxford University Press (OUP)
Date: 18-02-2011
Abstract: The Southeast Asian Sunda archipelago harbors a rich bio ersity with a substantial proportion of endemic species. The evolutionary history of these species has been drastically influenced by environmental forces, such as fluctuating sea levels, climatic changes, and severe volcanic activities. Orangutans (genus: Pongo), the only Asian great apes, are well suited to study the relative impact of these forces due to their well-documented behavioral ecology, strict habitat requirements, and exceptionally slow life history. We investigated the phylogeographic patterns and evolutionary history of orangutans in the light of the complex geological and climatic history of the Sunda archipelago. Our study is based on the most extensive genetic s ling to date, covering the entire range of extant orangutan populations. Using data from three mitochondrial DNA (mtDNA) genes from 112 wild orangutans, we show that Sumatran orangutans, Pongo abelii, are paraphyletic with respect to Bornean orangutans (P. pygmaeus), the only other currently recognized species within this genus. The deepest split in the mtDNA phylogeny of orangutans occurs across the Toba caldera in northern Sumatra and, not as expected, between both islands. Until the recent past, the Toba region has experienced extensive volcanic activity, which has shaped the current phylogeographic patterns. Like their Bornean counterparts, Sumatran orangutans exhibit a strong, yet previously undocumented structuring into four geographical clusters. However, with 3.50 Ma, the Sumatran haplotypes have a much older coalescence than their Bornean counterparts (178 kya). In sharp contrast to the mtDNA data, 18 Y-chromosomal polymorphisms show a much more recent coalescence within Sumatra compared with Borneo. Moreover, the deep geographic structure evident in mtDNA is not reflected in the male population history, strongly suggesting male-biased dispersal. We conclude that volcanic activities have played an important role in the evolutionary history of orangutans and potentially of many other forest-dwelling Sundaland species. Furthermore, we demonstrate that a strong sex bias in dispersal can lead to conflicting patterns in uniparentally inherited markers even at a genus-wide scale, highlighting the need for a combined usage of maternally and paternally inherited marker systems in phylogenetic studies.
Publisher: Wiley
Date: 2015
DOI: 10.1111/MEC.13027
Abstract: Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive s le set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: Proceedings of the National Academy of Sciences
Date: 22-11-2010
Abstract: Sundaland, a tropical hotspot of bio ersity comprising Borneo and Sumatra among other islands, the Malay Peninsula, and a shallow sea, has been subject to dramatic environmental processes. Thus, it presents an ideal opportunity to investigate the role of environmental mechanisms in shaping species distribution and ersity. We investigated the population structure and underlying mechanisms of an insular endemic, the Bornean orangutan ( Pongo pygmaeus ). Phylogenetic reconstructions based on mtDNA sequences from 211 wild orangutans covering the entire range of the species indicate an unexpectedly recent common ancestor of Bornean orangutans 176 ka (95% highest posterior density, 72–322 ka), pointing to a Pleistocene refugium. High mtDNA differentiation among populations and rare haplotype sharing is consistent with a pattern of strong female philopatry. This is corroborated by isolation by distance tests, which show a significant correlation between mtDNA ergence and distance and a strong effect of rivers as barriers for female movement. Both frequency-based and Bayesian clustering analyses using as many as 25 nuclear microsatellite loci revealed a significant separation among all populations, as well as a small degree of male-mediated gene flow. This study highlights the unique effects of environmental and biological features on the evolutionary history of Bornean orangutans, a highly endangered species particularly vulnerable to future climate and anthropogenic change as an insular endemic.
Publisher: Wiley
Date: 31-05-2012
No related grants have been discovered for Natasha Arora.