ORCID Profile
0000-0002-4805-5575
Current Organisation
University of Bern
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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: Proceedings of the National Academy of Sciences
Date: 30-01-2017
Abstract: The rate of genomic adaptation is determined by the rate of environmental change, the availability of beneficial mutations, and the efficiency of positive selection. The relative importance of these factors has been actively discussed. We address the questions using whole genome sequences of great apes, which have very different population sizes whereas their genomic architectures are highly similar. We infer that the impact of selection on the genomic ersity of a species increases with the effective population size, most likely due to the differential influx rate of beneficial mutations. This explanation is, among other possibilities, expected if adaptive evolution is limited by the waiting time for new favorable mutations in great apes.
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: 12-06-2012
Publisher: Wiley
Date: 12-10-2009
DOI: 10.1111/J.1755-0998.2009.02736.X
Abstract: The polyandrous fly Sepsis cynipsea has been used extensively in studies of sexual selection and local adaptation. We isolated and characterized 11 novel microsatellite markers for S. cynipsea from a genomic library and screened 32 flies for polymorphism. All microsatellite markers show high allelic ersity with an average of 9.64 alleles per locus. Two microsatellites were found likely to be X-linked. These novel markers will significantly advance studies of sexual selection and evolutionary genetics of S. cynipsea and related species, especially given the low numbers of markers currently available in this family.
Publisher: Wiley
Date: 06-01-2021
DOI: 10.1111/MEC.15774
Publisher: Wiley
Date: 05-07-2017
DOI: 10.1111/MEC.14197
Abstract: Recombination rate is heterogeneous across the genome of various species and so are genetic ersity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent ergence (<1 million years). Genetic ersity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.
Publisher: Elsevier BV
Date: 11-2017
DOI: 10.1016/J.CUB.2017.09.047
Abstract: Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru in idual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 in iduals survive. VIDEO ABSTRACT.
Publisher: Springer Science and Business Media LLC
Date: 15-11-2018
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: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.GDE.2016.09.005
Abstract: The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more ergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.
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: 28-06-2008
DOI: 10.1111/J.1755-0998.2008.02090.X
Abstract: We developed 16 novel polymorphic tetranucleotide microsatellite markers for Poecilia parae, a livebearing fish used in evolutionary studies because of its Y-linked colour and size polymorphism. A set of 199 clones was sequenced out of an enriched genomic library, and we achieved an enrichment efficiency of nearly 80%. Primers were designed for 16 pure repeats, and 59 P. parae were screened for polymorphism. Cross- lification was tested on Poecilia picta and Poecilia reticulata, the guppy. The new microsatellite markers showed an exceptionally high allelic ersity and low stutter formation, proving their suitability for a broad range of applications in these species.
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2015
Abstract: Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of erging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands how the differentiation landscape evolves as speciation advances and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence ergence ( d xy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in ersity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.
Publisher: Wiley
Date: 12-02-2009
DOI: 10.1111/J.1755-0998.2008.02246.X
Abstract: We isolated and characterized 19 novel tetranucleotide microsatellite markers in the Indo-Pacific bottlenose dolphin (Tursiops aduncus) in order to improve genotyping accuracy in applications like large-scale population-wide paternity and relatedness assessments. One hundred T. aduncus from Shark Bay, Western Australia, were screened for polymorphism. Cross- lification was tested on four other small odontocete species. The new tetranucleotide microsatellite loci showed a more than fourfold higher scoring accuracy and significantly lower stutter formation compared to eight dinucleotide loci, although overall allelic ersity was significantly reduced.
Publisher: Oxford University Press (OUP)
Date: 17-07-2015
Publisher: Wiley
Date: 31-05-2012
No related grants have been discovered for Alexander Nater.