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Brown LM, Elbon MC, Bharadwaj A, Damle G, Lachance J. Does Effective Population Size Govern Evolutionary Differences in Telomere Length? Genome Biol Evol 2024; 16:evae111. [PMID: 38771124 PMCID: PMC11140418 DOI: 10.1093/gbe/evae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Lengths of telomeres vary by an order of magnitude across mammalian species. Similarly, age- and sex-standardized telomere lengths differ by up to 1 kb (14%) across human populations. How to explain these differences? Telomeres play a central role in senescence and aging, and genes that affect telomere length are likely under weak selection (i.e. telomere length is a trait that is subject to nearly neutral evolution). Importantly, natural selection is more effective in large populations than in small populations. Here, we propose that observed differences in telomere length across species and populations are largely due to differences in effective population sizes. In this perspective, we present preliminary evolutionary genetic evidence supporting this hypothesis and highlight the need for more data.
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Affiliation(s)
- Lyda M Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mia C Elbon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ajay Bharadwaj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gargi Damle
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Mörchen J, Luhn F, Wassmer O, Kunz JA, Kulik L, van Noordwijk MA, Rianti P, Rahmaeti T, Utami Atmoko SS, Widdig A, Schuppli C. Orangutan males make increased use of social learning opportunities, when resource availability is high. iScience 2024; 27:108940. [PMID: 38333693 PMCID: PMC10850741 DOI: 10.1016/j.isci.2024.108940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/05/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Humans' colonization of diverse habitats relied on our ancestors' abilities to innovate and share innovations with others. While ecological impacts on innovations are well studied, their effect on social learning remains poorly understood. We examined how food availability affects social learning in migrant orangutan unflanged males, who may learn from local orangutans through peering (i.e., observational social learning). We analyzed 1,384 dyadic associations, including 360 peering events, among 46 wild Sumatran orangutan and 25 Bornean orangutan males, collected over 18 years. Migrants' peering rates significantly increased with higher food availability and time spent in proximity to others. Furthermore, migrants in the more sociable Sumatran population exhibited significantly higher peering rates compared to the Borneans, suggesting intrinsic and/or developmental effects of food availability on social learning. These findings emphasize the importance of investigating ecological effects on social learning on the immediate, developmental, and intrinsic levels for our understanding of cultural evolution.
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Affiliation(s)
- Julia Mörchen
- Development and Evolution of Cognition Research Group, Max Planck Institute of Animal Behavior, 78467 Konstanz, Germany
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
- Department of Primate Behaviour and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Frances Luhn
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Olivia Wassmer
- Department of Evolutionary Anthropology, University of Zurich, 8057 Zurich, Switzerland
| | - Julia A. Kunz
- Department of Evolutionary Anthropology, University of Zurich, 8057 Zurich, Switzerland
- Institute of Evolutionary Biology of Montpellier (ISEM), University of Montpellier, CNRS, IRD, 34095 Montpellier, France
| | - Lars Kulik
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Maria A. van Noordwijk
- Department of Evolutionary Anthropology, University of Zurich, 8057 Zurich, Switzerland
- Comparative Socioecology, Max Planck Institute of Animal Behavior, 78467 Konstanz, Germany
| | - Puji Rianti
- Primate Research Center, Institute of Research and Community Service, IPB University, Bogor 16680, Indonesia
- Animal Biosystematics and Ecology Division, Department of Biology, IPB University, Bogor 16680, Indonesia
| | - Tri Rahmaeti
- Department of Biology, Graduate Program, Faculty of Biology and Agriculture, Universitas Nasional, Jakarta 12520, Indonesia
| | - Sri Suci Utami Atmoko
- Department of Biology, Graduate Program, Faculty of Biology and Agriculture, Universitas Nasional, Jakarta 12520, Indonesia
| | - Anja Widdig
- Behavioral Ecology Research Group, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
- Department of Primate Behaviour and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Caroline Schuppli
- Development and Evolution of Cognition Research Group, Max Planck Institute of Animal Behavior, 78467 Konstanz, Germany
- Department of Evolutionary Anthropology, University of Zurich, 8057 Zurich, Switzerland
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Arekar K, Tiwari N, Sathyakumar S, Khaleel M, Karanth P. Geography vs. past climate: the drivers of population genetic structure of the Himalayan langur. BMC Ecol Evol 2022; 22:100. [PMID: 35971061 PMCID: PMC9377076 DOI: 10.1186/s12862-022-02054-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Contemporary species distribution, genetic diversity and evolutionary history in many taxa are shaped by both historical and current climate as well as topography. The Himalayas show a huge variation in topography and climatic conditions across its entire range, and have experienced major climatic fluctuations in the past. However, very little is known regarding how this heterogenous landscape has moulded the distribution of Himalayan fauna. A recent study examined the effect of these historical events on the genetic diversity of the Himalayan langurs in Nepal Himalaya. However, this study did not include the samples from the Indian Himalayan region (IHR). Therefore, here we revisit the questions addressed in the previous study with a near complete sampling from the IHR, along with the samples from the Nepal Himalaya. We used the mitochondrial Cytochrome-b (Cyt-b, 746 bp) region combined with multiple phylogeographic analyses and palaeodistribution modelling. Results Our dataset contained 144 sequences from the IHR as well as the Nepal Himalaya. Phylogenetic analysis showed a low divergent western clade nested within high divergent group of eastern lineages and in the network analysis we identified 22 haplotypes over the entire distribution range of the Himalayan langurs. Samples from the Nepal Himalaya showed geographically structured haplotypes corresponding to different river barriers, whereas samples from IHR showed star-like topology with no structure. Our statistical phylogeography analysis using diyABC supported the model of east to west colonisation of these langurs with founder event during colonisation. Analysis of demographic history showed that the effective population size of the Himalayan langurs decreased at the onset of last glacial maximum (LGM) and started increasing post LGM. The palaeodistribution modelling showed that the extent of suitable habitat shifted from low elevation central Nepal, and adjoining parts of north India, during LGM to the western Himalaya at present. Conclusion The current genetic diversity and distribution of Himalayan langurs in the Nepal Himalaya has been shaped by river barriers, whereas the rivers in the IHR had relatively less time to act as a strong genetic barrier after the recent colonisation event. Further, the post LGM expansion could have had confounding effect on Himalayan langur population structure in both Nepal Himalaya and IHR. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02054-1.
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“Engaging the Enemy”: Orangutan (Pongo pygmaeus morio) Conservation in Human Modified Environments in the Kinabatangan floodplain of Sabah, Malaysian Borneo. INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00288-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
Throughout the equatorial tropics, forest conversion to agriculture often fragments crucial primate habitat. In 30 years, 80% of the alluvial lowland forests along the Kinabatangan River in Sabah, Malaysian Borneo, have been supplanted by oil palm (Elaeis guineensis) plantations. Today, only about 20% of the former orangutan (Pongo pygmaeus morio) population remains in the region. Because most of the land is now under the tenure of agribusiness companies, we used a pragmatic approach of mixed biosocial methods and citizen science engagement of oil palm growers (N = 6) as active conservation partners to study orangutan use of the privately administered landscape between protected forest fragments. We found that 22 of 25 remanent forest patches (0.5 to 242 hectares) surveyed within plantations contained food or shelter resources useful for orangutans. Of these, 20 are in regular transitory use by wider-ranging adult male orangutans, and in 9 patches, females are resident and raising offspring isolated within oil palm plantations. These findings indicate that orangutans retain a measure of normal metapopulation dynamics necessary for viability at the landscape level despite drastic habitat modification. We found that barriers to in situ conservation in these agroforest matrices were due to the following misconceptions across sectors: 1) Good farming practices require exclusion of wildlife; 2) Orangutans seen in plantations must be “rescued” by people; and 3) Translocation is an appropriate conservation strategy, and nondetrimental to orangutans. Our exploratory study exemplifies the value of biosocial methods and collaboration with industrial-scale farmers to support primate resilience in forests fragmented by agriculture.
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Voicu AA, Krützen M, Bilgin Sonay T. Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution. FRONTIERS IN BIOINFORMATICS 2021; 1:695784. [PMID: 36303734 PMCID: PMC9581056 DOI: 10.3389/fbinf.2021.695784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.
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Affiliation(s)
| | - Michael Krützen
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Tugce Bilgin Sonay
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
- *Correspondence: Tugce Bilgin Sonay,
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Shin J, Jung J. Comparative population genetics of the invasive mosquito Aedes albopictus and the native mosquito Aedes flavopictus in the Korean peninsula. Parasit Vectors 2021; 14:377. [PMID: 34315478 PMCID: PMC8314453 DOI: 10.1186/s13071-021-04873-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aedes mosquitoes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, zika virus, and other dangerous vector-borne diseases. Aedes albopictus is native to southeast Asia, with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula. Aedes flavopictus is considered to be native to East Asia, with a broad distribution in the region, including the Korean peninsula. A better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control. METHODS We obtained DNA from 148 specimens of Ae. albopictus and 166 specimens of Ae. flavopictus in Korea, and amplified two mitochondrial genes (COI and ND5) to compare the genetic diversity and structure of the two species. RESULTS We obtained a 658-bp sequence of COI and a 423-bp sequence of ND5 from both mosquito species. We found low diversity and a nonsignificant population genetic structure in Ae. albopictus, and high diversity and a nonsignificant structure in Ae. flavopictus for these two mitochondrial genes. Aedes albopictus had fewer haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast, Ae. flavopictus had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was nonsignificant, Ae. flavopictus exhibited higher genetic diversity than Ae. albopictus. CONCLUSIONS Aedes albopictus appears to be an introduced species, whereas Ae. flavopictus is endemic to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. Further studies on the genetic structure and diversity of these mosquitos will provide useful data for vector control.
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Affiliation(s)
- Jiyeong Shin
- The Division of EcoCreative, Ewha Womans University, Seoul, 03760 South Korea
| | - Jongwoo Jung
- The Division of EcoCreative, Ewha Womans University, Seoul, 03760 South Korea
- Department of Science Education, Ewha Womans University, Seoul, 03760 South Korea
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Amano N, Wang YV, Boivin N, Roberts P. 'Emptying Forests?' Conservation Implications of Past Human-Primate Interactions. Trends Ecol Evol 2021; 36:345-359. [PMID: 33431163 DOI: 10.1016/j.tree.2020.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023]
Abstract
Non-human primates are among the most vulnerable tropical animals to extinction and ~50% of primate species are endangered. Human hunting is considered a major cause of increasingly 'empty forests', yet archaeological data remains under-utilised in testing this assertion over the longer-term. Zooarchaeological datasets allow investigation of human exploitation of primates and the reconstruction of extinction, extirpation, and translocation processes. We evaluate the application and limitations of data from zooarchaeological studies spanning the past 45 000 years in South and Southeast Asia in guiding primate conservation efforts. We highlight that environmental change was the primary threat to many South and Southeast Asian non-human primate populations during much of the Holocene, foreshadowing human-induced land-use and environmental change as major threats of the 21st century.
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Affiliation(s)
- Noel Amano
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Yiming V Wang
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
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The historical range and drivers of decline of the Tapanuli orangutan. PLoS One 2021; 16:e0238087. [PMID: 33395430 PMCID: PMC7781382 DOI: 10.1371/journal.pone.0238087] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/20/2020] [Indexed: 11/19/2022] Open
Abstract
The Tapanuli Orangutan (Pongo tapanuliensis) is the most threatened great ape species in the world. It is restricted to an area of about 1,000 km2 of upland forest where fewer than 800 animals survive in three declining subpopulations. Through a historical ecology approach involving analysis of newspaper, journals, books and museum records from the early 1800s to 2009, we demonstrate that historically Pongo tapanuliensis inhabited a much larger area, and occurred across a much wider range of habitat types and at lower elevations than now. Its current Extent of Occurrence is 2.5% and 5.0% of the historical range in the 1890s and 1940s respectively. A combination of historical fragmentation of forest habitats, mostly for small-scale agriculture, and unsustainable hunting likely drove various populations to the south, east and west of the current population to extinction. This happened prior to the industrial-scale forest conversion that started in the 1970s. Our findings indicate how sensitive P. tapanuliensis is to the combined effects of habitat fragmentation and unsustainable take-off rates. Saving this species will require prevention of any further fragmentation and killings or other removal of animals from the remaining population. Without concerted action to achieve this, the remaining populations of P. tapanuliensis are doomed to become extinct within several orangutan generations.
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Banes GL, Fountain ED, Karklus A, Huang HM, Jang-Liaw NH, Burgess DL, Wendt J, Moehlenkamp C, Mayhew GF. Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo). BMC Genomics 2020; 21:873. [PMID: 33287706 PMCID: PMC7720378 DOI: 10.1186/s12864-020-07278-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery approach, combining data from published whole-genome sequences, novel whole-exome sequencing, and microarray-derived genotype data, we aimed to develop a highly informative gene-focused panel of targets that can be used to address a broad range of research questions. RESULTS We identified and present genomic co-ordinates for 175,186 SNPs and 2315 Y-chromosomal targets, plus 185 genes either known or presumed to be pathogenic in cardiovascular (N = 109) or respiratory (N = 43) diseases in humans - the primary and secondary causes of captive orang-utan mortality - or a majority of other human diseases (N = 33). As proof of concept, we designed and synthesized 'SeqCap' hybrid capture probes for these targets, demonstrating cost-effective target enrichment and reduced-representation sequencing. CONCLUSIONS Our targets are of broad utility in studies of orang-utan ancestry, admixture and disease susceptibility and aetiology, and thus are of value in addressing questions key to the survival of these species. To facilitate comparative analyses, these targets could now be standardized for future orang-utan population genomic studies. The targets are broadly compatible with commercial target enrichment platforms and can be utilized as published here to synthesize applicable probes.
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Affiliation(s)
- Graham L Banes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA.
| | - Emily D Fountain
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA
| | - Alyssa Karklus
- School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA
| | - Hao-Ming Huang
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Daniel L Burgess
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Polymer Forge, Inc., 504 S Rosa Rd Ste 200, Madison, WI, 53719, USA
| | - Jennifer Wendt
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Promega Corporation, 2800 Woods Hollow Rd, Fitchburg, WI, 53711, USA
| | - Cynthia Moehlenkamp
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Exact Sciences, 441 Charmany Dr, Madison, WI, 53719, USA
| | - George F Mayhew
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
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Wang XY, Wang MM, Chen C, Wang XQ. Genetic variation and phylogeographic structure of Spodoptera exigua in western China based on mitochondrial DNA and microsatellite markers. PLoS One 2020; 15:e0233133. [PMID: 32407374 PMCID: PMC7224464 DOI: 10.1371/journal.pone.0233133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/28/2020] [Indexed: 11/19/2022] Open
Abstract
The beet armyworm, Spodoptera exigua, is a significant agricultural pest of numerous crops and has caused serious economic losses in China. To effectively control this pest, we analyzed its genetic variation, population genetic structure and demographic history. We used mitochondrial DNA (mtDNA) fragments of the cytochrome oxidase subunit I (COI) and eight nuclear microsatellite loci to investigate genetic diversity and population genetic structure of S. exigua populations at 14 sampling sites in western China. Both mtDNA and microsatellite data indicated low levels of genetic diversity among all populations. A moderate genetic differentiation among some S. exigua populations was detected. Neighbor-joining dendrograms, STRUCTURE, and principal coordinate analysis (PCoA) revealed two genetically distinct groups: the KEL group and the remaining population group. Isolation by distance (IBD) results showed a weak significant correlation between geographic distance and genetic differentiation. Haplotype networks, neutrality testing, and mismatch distribution analysis indicated that the beet armyworm experienced a recent rapid expansion without a recent genetic bottleneck in western China. Thus, the results of this population genetic study can help with the development of strategies for managing this highly migratory pest.
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Affiliation(s)
- Xing-Ya Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Ming-Ming Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chen Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiao-Qi Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
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Home range establishment and the mechanisms of philopatry among female Bornean orangutans (Pongo pygmaeus wurmbii) at Tuanan. Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-2818-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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van Noordwijk MA, Utami Atmoko SS, Knott CD, Kuze N, Morrogh-Bernard HC, Oram F, Schuppli C, van Schaik CP, Willems EP. The slow ape: High infant survival and long interbirth intervals in wild orangutans. J Hum Evol 2018; 125:38-49. [PMID: 30502896 DOI: 10.1016/j.jhevol.2018.09.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/14/2018] [Accepted: 09/20/2018] [Indexed: 11/17/2022]
Abstract
Orangutans (Pongo spp.) are reported to have extremely slow life histories, including the longest average interbirth intervals of all mammals. Such slow life history can be viable only when unavoidable mortality is kept low. Thus, orangutans' survivorship under natural conditions is expected to be extremely high. Previous estimates of orangutan life history were based on captive individuals living under very different circumstances or on small samples from wild populations. Here, we combine birth data from seven field sites, each with demographic data collection for at least 10 years (range 12-43 years) on wild orangutans to better document their life history. Using strict criteria for data inclusion, we calculated infant survival, interbirth intervals and female age at first reproduction, across species, subspecies and islands. We found an average closed interbirth interval of 7.6 years, as well as consistently very high pre-weaning survival for males and females. Female survival of 94% until age at first birth (at around age 15 years) was higher than reported for any other mammal species under natural conditions. Similarly, annual survival among parous females is very high, but longevity remains to be estimated. Current data suggest no major life history differences between Sumatran and Bornean orangutans. The high offspring survival is remarkable, noting that modern human populations seem to have reached the same level of survival only in the 20th century. The orangutans' slow life history illustrates what can be achieved if a hominoid bauplan is exposed to low unavoidable mortality. Their high survival is likely due to their arboreal and non-gregarious lifestyle, and has allowed them to maintain viable populations, despite living in low-productivity habitats. However, their slow life history also implies that orangutans are highly vulnerable to a catastrophic population crash in the face of drastic habitat change.
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Affiliation(s)
- Maria A van Noordwijk
- Department of Anthropology, University of Zürich, Winterthurerstr 190, 8057, Zürich, Switzerland.
| | - S Suci Utami Atmoko
- Fakultas Biologi, Universitas Nasional, Jln Sawo Manila, Jakarta, 12520, Indonesia
| | - Cheryl D Knott
- Department of Anthropology, Boston University, Boston, MA, 02215, USA
| | - Noko Kuze
- Department of Anthropology, The National Museum of Nature and Science, Ibaraki, 305-0005, Japan
| | - Helen C Morrogh-Bernard
- Borneo Nature Foundation, Palangkaraya 73112, Indonesia; College of Life and Environmental Science, University of Exeter, Cornwall, TR10 9FE, England, UK
| | - Felicity Oram
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia; HUTAN-Kinabatangan Orangutan Conservation Programme Sandakan, Sabah, 88999, Malaysia
| | - Caroline Schuppli
- Department of Anthropology, University of Zürich, Winterthurerstr 190, 8057, Zürich, Switzerland
| | - Carel P van Schaik
- Department of Anthropology, University of Zürich, Winterthurerstr 190, 8057, Zürich, Switzerland
| | - Erik P Willems
- Department of Anthropology, University of Zürich, Winterthurerstr 190, 8057, Zürich, Switzerland
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Abstract
In humans, patterns of cranial variation mirror genetic diversity globally, implicating population history as a key driver of cranial disparity. Here, we demonstrate that the magnitude of genetic diversity within 12 extant ape taxa explains a large proportion of cranial shape variation. Taxa that are more genetically diverse tend to be more cranially diverse also. Our results suggest that neutral evolutionary processes such as mutation, genetic drift, and gene flow are reflected in both genetic and cranial diversity in apes. This work provides a perspective on intraspecific cranial variation in apes which has important implications for interpreting selective and developmental pressures on the cranium and for understanding shape variation in fossil hominin crania. Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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15
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McCarthy MS, Lester JD, Langergraber KE, Stanford CB, Vigilant L. Genetic analysis suggests dispersal among chimpanzees in a fragmented forest landscape in Uganda. Am J Primatol 2018; 80:e22902. [PMID: 30052284 DOI: 10.1002/ajp.22902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/05/2022]
Abstract
Habitat fragmentation is a leading threat to global biodiversity. Dispersal plays a key role in gene flow and population viability, but the impact of fragmentation on dispersal patterns remains poorly understood. Among chimpanzees, males typically remain in their natal communities while females often disperse. However, habitat loss and fragmentation may cause severe ecological disruptions, potentially resulting in decreased fitness benefits of male philopatry and limited female dispersal ability. To investigate this issue, we genotyped nearly 900 non-invasively collected chimpanzee fecal samples across a fragmented forest habitat that may function as a corridor between two large continuous forests in Uganda, and used the spatial associations among co-sampled genotypes to attribute a total of 229 individuals to 10 distinct communities, including 9 communities in the corridor habitat and 1 in continuous forest. We then used parentage analyses to infer instances of between-community dispersal. Of the 115 parent-offspring dyads detected with confidence, members of 39% (N = 26) of mother-daughter dyads were found in different communities, while members of 10% (N = 5) of father-son dyads were found in different communities. We also found direct evidence for one dispersal event that occurred during the study period, as a female's sample found first in one community was found multiple times in another community 19 months later. These findings suggest that even in fragmented habitats, chimpanzee males remain in their natal communities while females tend to disperse. Corridor enhancement in unprotected forest fragments could help maintain gene flow in chimpanzees and other species amid anthropogenic pressures.
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Affiliation(s)
- Maureen S McCarthy
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute of Human Origins, Arizona State University, Tempe, Arizona
| | - Craig B Stanford
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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16
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Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 2017; 18:319-333. [PMID: 29058768 PMCID: PMC5900898 DOI: 10.1111/1755-0998.12728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
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Affiliation(s)
- Jessica Hernandez-Rodriguez
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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17
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Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. Curr Biol 2017; 27:3487-3498.e10. [PMID: 29103940 DOI: 10.1016/j.cub.2017.09.047] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/17/2017] [Accepted: 09/20/2017] [Indexed: 12/30/2022]
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 individual 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 individuals survive. VIDEO ABSTRACT.
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Affiliation(s)
- Alexander Nater
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
| | - Maja P Mattle-Greminger
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Anton Nurcahyo
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Matthew G Nowak
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Department of Anthropology, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Marc de Manuel
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Colin Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tugce Bilgin Sonay
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Adriano R Lameira
- Department of Anthropology, Durham University, Dawson Building, South Road, Durham DH1 3LE, UK; School of Psychology & Neuroscience, St. Andrews University, St. Mary's Quad, South Street, St. Andrews, Fife KY16 9JP, Scotland, UK
| | - Serge A Wich
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - James Askew
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Marina Davila-Ross
- Department of Psychology, University of Portsmouth, King Henry Building, King Henry 1(st) Street, Portsmouth PO1 2DY, UK
| | - Gabriella Fredriksson
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - Guillem de Valles
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Ferran Casals
- Servei de Genòmica, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | | | - Benoit Goossens
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff CF10 3BA, UK
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288GJ Rijswijk, the Netherlands
| | - Kristin S Warren
- Conservation Medicine Program, College of Veterinary Medicine, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Ian Singleton
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Foundation for a Sustainable Ecosystem (YEL), Medan, Indonesia
| | - David A Marques
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Joko Pamungkas
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Faculty of Veterinary Medicine, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Puji Rianti
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Carel P van Schaik
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Erik Meijaard
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia; Borneo Futures, Bandar Seri Begawan, Brunei Darussalam.
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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18
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Reid MJC, Switzer WM, Schillaci MA, Klegarth AR, Campbell E, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Hollocher H, Sandstrom PA, Brooks JI. Bayesian inference reveals ancient origin of simian foamy virus in orangutans. INFECTION GENETICS AND EVOLUTION 2017; 51:54-66. [PMID: 28274887 DOI: 10.1016/j.meegid.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/25/2017] [Accepted: 03/03/2017] [Indexed: 02/08/2023]
Abstract
Simian foamy viruses (SFVs) infect most nonhuman primate species and appears to co-evolve with its hosts. This co-evolutionary signal is particularly strong among great apes, including orangutans (genus Pongo). Previous studies have identified three distinct orangutan SFV clades. The first of these three clades is composed of SFV from P. abelii from Sumatra, the second consists of SFV from P. pygmaeus from Borneo, while the third clade is mixed, comprising an SFV strain found in both species of orangutan. The existence of the mixed clade has been attributed to an expansion of P. pygmaeus into Sumatra following the Mount Toba super-volcanic eruption about 73,000years ago. Divergence dating, however, has yet to be performed to establish a temporal association with the Toba eruption. Here, we use a Bayesian framework and a relaxed molecular clock model with fossil calibrations to test the Toba hypothesis and to gain a more complete understanding of the evolutionary history of orangutan SFV. As with previous studies, our results show a similar three-clade orangutan SFV phylogeny, along with strong statistical support for SFV-host co-evolution in orangutans. Using Bayesian inference, we date the origin of orangutan SFV to >4.7 million years ago (mya), while the mixed species clade dates to approximately 1.7mya, >1.6 million years older than the Toba super-eruption. These results, combined with fossil and paleogeographic evidence, suggest that the origin of SFV in Sumatran and Bornean orangutans, including the mixed species clade, likely occurred on the mainland of Indo-China during the Late Pliocene and Calabrian stage of the Pleistocene, respectively.
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Affiliation(s)
- Michael J C Reid
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
| | - Amy R Klegarth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Anthropology, University of Washington, Seattle, WA 98105, USA.
| | - Ellsworth Campbell
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Manon Ragonnet-Cronin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom
| | - Isabelle Joanisse
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kyna Caminiti
- Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada.
| | - Carl A Lowenberger
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Birute Mary F Galdikas
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA
| | - Hope Hollocher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Paul A Sandstrom
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada.
| | - James I Brooks
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; The Ottawa Hospital, Division of Infectious Diseases, Department of Medicine, University of Ottawa, 1053 Carling Ave., Ottawa, ONK1Y 4E9, Canada
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19
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Abstract
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes.
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20
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Banes GL, Galdikas BMF. Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions. PLoS One 2016; 11:e0168715. [PMID: 28033350 PMCID: PMC5199090 DOI: 10.1371/journal.pone.0168715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/04/2016] [Indexed: 11/18/2022] Open
Abstract
The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however-particularly, in some species, in other understudied hypervariable regions. To assess the abundance and utility of such potential variations in orang-utans, we characterised 36 complete control-region haplotypes, of which 13 were of Sumatran and 23 of Bornean maternal ancestry, and compared polymorphisms within these and within shorter HVRI segments predominantly analysed in prior phylogenetic studies of Sumatran (~385 bp) and Bornean (~323 bp) orang-utans. We amplified the complete control region in a single PCR that proved successful even with highly degraded, non-invasive samples. By using species-specific primers to produce a single large amplicon (~1600 bp) comprising flanking coding regions, our method also serves to better avoid amplification of nuclear mitochondrial insertions (numts). We found the number, length and position of hypervariable regions is inconsistent between orang-utan species, and that prior definitions of the HVRI were haphazard. Polymorphisms occurring outside the predominantly analysed segments were phylogeographically informative in isolation, and could be used to assign haplotypes to comparable clades concordant with geographic subpopulations. The predominantly analysed segments could discern only up to 76% of all haplotypes, highlighting the forensic utility of complete control-region sequences. In the face of declining sequencing costs and our proven application to poor-quality DNA extracts, we see no reason to ever amplify only specific 'hypervariable regions' in any taxa, particularly as their lengths and positions are inconsistent and cannot be reliably defined-yet this strategy predominates widely. Given their greater utility and consistency, we instead advocate analysis of complete control-region sequences in future studies, where any shorter segment might otherwise have proven the region of choice.
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Affiliation(s)
- Graham L. Banes
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- CAS-MPG Partner Institute for Computational Biology, Shanghai, People’s Republic of China
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21
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Kanamori T, Kuze N, Bernard H, Malim TP, Kohshima S. Fluctuations of population density in Bornean orangutans (Pongo pygmaeus morio) related to fruit availability in the Danum Valley, Sabah, Malaysia: a 10-year record including two mast fruitings and three other peak fruitings. Primates 2016; 58:225-235. [DOI: 10.1007/s10329-016-0584-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/25/2016] [Indexed: 11/30/2022]
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Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. Evolution and demography of the great apes. Curr Opin Genet Dev 2016; 41:124-129. [PMID: 27716526 DOI: 10.1016/j.gde.2016.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/27/2023]
Abstract
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent 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.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Alexander Nater
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maja P Greminger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
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Osada N. Genetic diversity in humans and non-human primates and its evolutionary consequences. Genes Genet Syst 2016; 90:133-45. [PMID: 26510568 DOI: 10.1266/ggs.90.133] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity is a key parameter in population genetics and is important for understanding the process of evolution and for the development of appropriate conservation strategies. Recent advances in sequencing technology have enabled the measurement of genetic diversity of various organisms at the nucleotide level and on a genome-wide scale, yielding more precise estimates than were previously achievable. In this review, I have compiled and summarized the estimates of genetic diversity in humans and non-human primates based on recent genome-wide studies. Although studies on population genetics demonstrated fluctuations in population sizes over time, general patterns have emerged. As shown previously, genetic diversity in humans is one of the lowest among primates; however, certain other primate species exhibit genetic diversity that is comparable to or even lower than that in humans. There exists greater than 10-fold variation in genetic diversity among primate species, and I found weak correlation with species fecundity but not with body or propagule size. I further discuss the potential evolutionary consequences of population size decline on the evolution of primate species. The level of genetic diversity negatively correlates with the ratio of non-synonymous to synonymous polymorphisms in a population, suggesting that proportionally greater numbers of slightly deleterious mutations segregate in small rather than large populations. Although population size decline is likely to promote the fixation of slightly deleterious mutations, there are molecular mechanisms, such as compensatory mutations at various molecular levels, which may prevent fitness decline at the population level. The effects of slightly deleterious mutations from theoretical and empirical studies and their relevance to conservation biology are also discussed in this review.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics
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Prevalence of Cryptosporidium spp., Enterocytozoon bieneusi, Encephalitozoon spp. and Giardia intestinalis in Wild, Semi-Wild and Captive Orangutans (Pongo abelii and Pongo pygmaeus) on Sumatra and Borneo, Indonesia. PLoS One 2016; 11:e0152771. [PMID: 27031241 PMCID: PMC4816420 DOI: 10.1371/journal.pone.0152771] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/18/2016] [Indexed: 11/19/2022] Open
Abstract
Background Orangutans are critically endangered primarily due to loss and fragmentation of their natural habitat. This could bring them into closer contact with humans and increase the risk of zoonotic pathogen transmission. Aims To describe the prevalence and diversity of Cryptosporidium spp., microsporidia and Giardia intestinalis in orangutans at seven sites on Sumatra and Kalimantan, and to evaluate the impact of orangutans’ habituation and location on the occurrence of these zoonotic protists. Result The overall prevalence of parasites in 298 examined animals was 11.1%. The most prevalent microsporidia was Encephalitozoon cuniculi genotype II, found in 21 animals (7.0%). Enterocytozoon bieneusi genotype D (n = 5) and novel genotype Pongo 2 were detected only in six individuals (2.0%). To the best of our knowledge, this is the first report of these parasites in orangutans. Eight animals were positive for Cryptosporidium spp. (2.7%), including C. parvum (n = 2) and C. muris (n = 6). Giardia intestinalis assemblage B, subtype MB6, was identified in a single individual. While no significant differences between the different human contact level groups (p = 0.479–0.670) or between the different islands (p = 0.992) were reported in case of E. bieneusi or E. cuniculi, Cryptosporidium spp. was significantly less frequently detected in wild individuals (p < 2×10−16) and was significantly more prevalent in orangutans on Kalimantan than on Sumatra (p < 2×10−16). Conclusion Our results revealed that wild orangutans are significantly less frequently infected by Cryptosporidium spp. than captive and semi-wild animals. In addition, this parasite was more frequently detected at localities on Kalimantan. In contrast, we did not detect any significant difference in the prevalence of microsporidia between the studied groups of animals. The sources and transmission modes of infections were not determined, as this would require repeated sampling of individuals, examination of water sources, and sampling of humans and animals sharing the habitat with orangutans.
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Wich SA, Singleton I, Nowak MG, Utami Atmoko SS, Nisam G, Arif SM, Putra RH, Ardi R, Fredriksson G, Usher G, Gaveau DLA, Kühl HS. Land-cover changes predict steep declines for the Sumatran orangutan (Pongo abelii). SCIENCE ADVANCES 2016; 2:e1500789. [PMID: 26973868 PMCID: PMC4783118 DOI: 10.1126/sciadv.1500789] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/07/2015] [Indexed: 05/05/2023]
Abstract
Positive news about Sumatran orangutans is rare. The species is critically endangered because of forest loss and poaching, and therefore, determining the impact of future land-use change on this species is important. To date, the total Sumatran orangutan population has been estimated at 6600 individuals. On the basis of new transect surveys, we estimate a population of 14,613 in 2015. This higher estimate is due to three factors. First, orangutans were found at higher elevations, elevations previously considered outside of their range and, consequently, not surveyed previously. Second, orangutans were found more widely distributed in logged forests. Third, orangutans were found in areas west of the Toba Lake that were not previously surveyed. This increase in numbers is therefore due to a more wide-ranging survey effort and is not indicative of an increase in the orangutan population in Sumatra. There are evidently more Sumatran orangutans remaining in the wild than we thought, but the species remains under serious threat. Current scenarios for future forest loss predict that as many as 4500 individuals could vanish by 2030. Despite the positive finding that the population is double the size previously estimated, our results indicate that future deforestation will continue to be the cause of rapid declines in orangutan numbers. Hence, we urge that all developmental planning involving forest loss be accompanied by appropriate environmental impact assessments conforming with the current national and provincial legislations, and, through these, implement specific measures to reduce or, better, avoid negative impacts on forests where orangutans occur.
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Affiliation(s)
- Serge A. Wich
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Byrom Street, L33AF Liverpool, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, Amsterdam 1098, Netherlands
- Corresponding author. E-mail:
| | - Ian Singleton
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
| | - Matthew G. Nowak
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
- Department of Anthropology, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Sri Suci Utami Atmoko
- Fakultas Biologi, Universitas Nasional, Jalan Sawo Manila, Pasar Minggu, Jakarta Selatan 12520, Indonesia
| | - Gonda Nisam
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
| | - Sugesti Mhd. Arif
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
| | - Rudi H. Putra
- Leuser Conservation Forum, Jalan Geuchik Raja No. 89 A, Banda Aceh 23233, Indonesia
| | - Rio Ardi
- Yayasan Orangutan Sumatera Lestari–Orangutan Information Centre, Jalan Bunga Sedap Malam 18C No. 10, Medan 20131, Indonesia
| | - Gabriella Fredriksson
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, Amsterdam 1098, Netherlands
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
| | - Graham Usher
- Sumatran Orangutan Conservation Programme, Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia
| | - David L. A. Gaveau
- Center for International Forestry Research, P.O. Box 0113 BOCBD, Bogor 16000, Indonesia
| | - Hjalmar S. Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 6, 04103 Leipzig, Germany
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Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.1016/j.hjb.2015.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Nater A, Greminger MP, Arora N, van Schaik CP, Goossens B, Singleton I, Verschoor EJ, Warren KS, Krützen M. Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation. Mol Ecol 2015; 24:310-27. [PMID: 25439562 DOI: 10.1111/mec.13027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/27/2022]
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 sample 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.
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Affiliation(s)
- Alexander Nater
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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Chakraborty D, Ramakrishnan U, Sinha A. Quaternary climate change and social behavior shaped the genetic differentiation of an endangered montane primate from the southern edge of the Tibetan Plateau. Am J Primatol 2014; 77:271-84. [DOI: 10.1002/ajp.22343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation; Mysore India
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
| | - Anindya Sinha
- Nature Conservation Foundation; Mysore India
- National Centre for Biological Sciences; Tata Institute of Fundamental Research; Bangalore India
- National Institute of Advanced Studies; Bangalore India
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Abstract
The great ape families are the species most closely related to our own, comprising chimpanzees, bonobos, gorillas, and orangutans. They live exclusively in tropical rainforests in Central Africa and the islands of Southeast Asia. Due to their close evolutionary relationship with humans, great apes share many cognitive, physiological, and morphological similarities with humans. The members of the great ape family make obvious models to facilitate the further understanding about humans' biology and history. This review will discuss how the recent addition of genome-wide data from great apes has furthered humans' understanding of these species and humanity, especially in the realm of evolutionary genetics.
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31
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Genetic diversity and population structure of sickleweed (Falcaria vulgaris; Apiaceae) in the upper Midwest USA. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0651-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Greminger MP, Stölting KN, Nater A, Goossens B, Arora N, Bruggmann R, Patrignani A, Nussberger B, Sharma R, Kraus RHS, Ambu LN, Singleton I, Chikhi L, van Schaik CP, Krützen M. Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. BMC Genomics 2014; 15:16. [PMID: 24405840 PMCID: PMC3897891 DOI: 10.1186/1471-2164-15-16] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 12/21/2013] [Indexed: 12/30/2022] Open
Abstract
Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance.
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Affiliation(s)
- Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, Zurich, Switzerland.
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Duan Y, Wu YQ, Luo LZ, Miao J, Gong ZJ, Jiang YL, Li T. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China. PLoS One 2013; 8:e78415. [PMID: 24265688 PMCID: PMC3827046 DOI: 10.1371/journal.pone.0078415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/20/2013] [Indexed: 11/17/2022] Open
Abstract
The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (FST = 0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (FST = 0.116, Nm = 1.89) than those in the eastern group (FST = 0.049, Nm = 4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.
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Affiliation(s)
- Yun Duan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People's Republic of China, Zhengzhou, China ; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
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Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One 2013; 8:e77175. [PMID: 24194868 PMCID: PMC3806739 DOI: 10.1371/journal.pone.0077175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 08/30/2013] [Indexed: 12/04/2022] Open
Abstract
To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.
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Affiliation(s)
- Xin Ma
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Joanna L. Kelley
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Kirsten Eilertson
- Bioinformatics Core, Gladstone Institutes, San Francisco, California, United States of America
| | - Shaila Musharoff
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jeremiah D. Degenhardt
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - André L. Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Tomas Vinar
- Department of Applied Informatics, Comenius University, Bratislava, Slovakia
| | - Carolin Kosiol
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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Gruber T. Uncovering the cultural knowledge of sanctuary apes. Commun Integr Biol 2013; 6:e23833. [PMID: 23713136 PMCID: PMC3656017 DOI: 10.4161/cib.23833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
Behavioral differences observed between wild communities of the same species have been called “cultures” by some researchers who aimed to underline the similarities with human cultures. However, whether these differences truly result from social learning processes is debated. Despite promising recent research, data acquired in the wild still fail to exclude genetic and ecological factors from being potential explanations for the observed behavioral differences. A potential way to address this problem is through field experiments where communities of the same subspecies are exposed to identical apparatuses. This way, genetic and ecological factors can be controlled for, although their influence cannot be fully excluded. Working with wild-born Sumatran orangutans originating from two genetically distinct populations, we recently combined field experiments with captive work to show that genetic differences could not account for differences in their knowledge of stick use. Additionally, we found evidence that our subjects arrived at the sanctuary with a knowledge that they acquired but could not express in their community of origin. These findings suggest that animal cultures must also be analyzed at the cognitive level. Only in this way can we understand the true extent of animal cultures and how they relate to human cultures.
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