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Dalui S, Sharma LK, Thakur M. Barriers and corridors: Assessment of gene flow and movement among red panda populations in eastern Himalayas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172523. [PMID: 38657804 DOI: 10.1016/j.scitotenv.2024.172523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of several meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale spatial genetic analysis to understand the contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within the protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang river in the central region, and the Dibang river, Lohit river, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We propose the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.
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Affiliation(s)
- Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India; Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053, India.
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Zhang L, Zhao ZW, Ma LX, Dong YW. Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172010. [PMID: 38575020 DOI: 10.1016/j.scitotenv.2024.172010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.
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Affiliation(s)
- Liang Zhang
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Zhan-Wei Zhao
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Lin-Xuan Ma
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Yun-Wei Dong
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China.
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Chromosome Evolution of the Liolaemus monticola (Liolaemidae) Complex: Chromosomal and Molecular Aspects. Animals (Basel) 2022; 12:ani12233372. [PMID: 36496893 PMCID: PMC9737244 DOI: 10.3390/ani12233372] [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: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosomal rearrangements can directly influence population differentiation and speciation. The Liolaemus monticola complex in Chile is a unique model consisting of several chromosome races arranged in a latitudinal sequence of increasing karyotype complexity from south to north. Here, we compared chromosomal and mitochondrial cytochrome b data from 15 localities across the northern geographic distribution of L. monticola. We expanded the distribution of the previously described Multiple Fissions race (re-described as MF2), in the Coastal range between the Aconcagua River and the Petorca River, and described a new Multiple Fissions 1 (MF1) race in the Andean range. Both races present centric fissions in pairs 1 and 2, as well as a pericentric inversion in one fission product of pair 2 that changes the NOR position. Additionally, we detected a new chromosomal race north of the Petorca River, the Northern Modified 2 (NM2) race, which is polymorphic for novel centric fissions in pairs 3 and 4. Our results increase the number of chromosomal races in L. monticola to seven, suggesting a complex evolutionary history of chromosomal rearrangements, population isolation by barriers, and hybridization. These results show the relevant role of chromosome mutations in evolution, especially for highly speciose groups such as Liolaemus lizards.
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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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Popadin K, Gunbin K, Peshkin L, Annis S, Fleischmann Z, Franco M, Kraytsberg Y, Markuzon N, Ackermann RR, Khrapko K. Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors. Genes (Basel) 2022; 13:810. [PMID: 35627195 PMCID: PMC9140377 DOI: 10.3390/genes13050810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/16/2022] [Indexed: 12/02/2022] Open
Abstract
The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).
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Affiliation(s)
- Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Leonid Peshkin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | | | | | - Rebecca R. Ackermann
- Human Evolution Research Institute, Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa;
| | - Konstantin Khrapko
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
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Estimating bonobo ( Pan paniscus) and chimpanzee ( Pan troglodytes) evolutionary history from nucleotide site patterns. Proc Natl Acad Sci U S A 2022; 119:e2200858119. [PMID: 35452306 PMCID: PMC9170072 DOI: 10.1073/pnas.2200858119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is genomic evidence of widespread admixture in deep time between many closely related species, including humans. Our closest living relatives, bonobos and chimpanzees, may also exhibit such patterns. However, assessing the exact degree of interbreeding remains challenging because previous studies have resulted in multiple inconsistent demographic models. We use an approach that addresses these gaps by analyzing all lineages, simultaneously estimating parameters, and comparing previously models. We find evidence of considerable introgression from western into eastern chimpanzees. We also show more breeding females than males and evidence of male-biased dispersal in western chimpanzees. These findings highlight the extent of admixture in bonobo and chimpanzee evolutionary history and are consistent with substantial differences between past and present chimpanzee biogeography. Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models. Here, we investigate this gap in knowledge using nucleotide site patterns calculated from whole-genome sequences from the autosomes of 71 bonobos and chimpanzees, representing all five extant Pan lineages. We estimated demographic parameters and compared all previously proposed demographic models for this clade. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. We show that 1) 21% of autosomal DNA in eastern chimpanzees derives from western chimpanzee introgression and that 2) all four chimpanzee lineages share a common ancestor about 987,000 y ago, much earlier than previous estimates. In addition, we suggest that 3) there was male reproductive skew throughout Pan evolutionary history and find evidence of 4) male-biased dispersal from western to eastern chimpanzees. Collectively, these results offer insight into bonobo and chimpanzee evolutionary history and suggest considerable differences between current and historic chimpanzee biogeography.
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Semen collection, evaluation, and cryopreservation in the bonobo (Pan paniscus). BMC ZOOL 2022; 7:12. [PMID: 37170297 PMCID: PMC10127325 DOI: 10.1186/s40850-022-00110-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 01/25/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Captive breeding of bonobos (Pan paniscus) has proven to be successful, but maintaining genetic diversity remains a challenge. Cryopreservation of semen is an important potential tool to maintain genetic diversity by preserving current genetic material for future use, as well as facilitating the transport and exchange of genetic material. This study aimed to develop a protocol for semen collection and cryopreservation in the bonobo. Semen was collected from four healthy adult bonobos under general anesthesia during management translocation procedures. Semen collection utilizing urethral catheterization was not successful (n = 1), however, all males (n = 4) responded well to rectal probe electro-ejaculation. Immediately after collection, ejaculates were evaluated for color and admixtures, volume, motility, and concentration. Eosin-Nigrosin staining was prepared to evaluate morphology and viability. Ejaculates were split into two equal volumes and cryopreserved in two different extenders, using a one-step and a two-step approach. Ejaculates were gradually cooled to 4 °C in two hours, subsequently stored in liquid nitrogen vapor for twenty minutes (0.25 ml straws), and finally dropped into liquid nitrogen.
Results
Pre-freeze evaluation showed thick, white samples with an average ejaculate volume of 450 µl (100-1000 µl), total motility of 59% (40–80%), viability of 69% (38–85%) and 58% (46–72%) normal spermatozoa. Mainly head (22%) and tail (19%) defects were detected on the Eosin-Nigrosin stain. Ejaculates were highly concentrated, nevertheless, due to the coagulum that caused high viscosity and non-homogenous fractions, only estimations of concentration could be made (1000 million/ml). After 24 h of storage, the post-thaw evaluation showed a loss of quality with an average post-thaw total motility of 15% (5–25%) using the one-step freezing medium, and 19% (5–30%) using the two-step medium. Average post-thaw viability was 15% (4–24%) and 21% (15–29%), respectively.
Conclusions
This report on ejaculates from bonobos obtained by rectal probe electro-ejaculation shows that semen parameters of this species are not completely similar to those of its sibling species, the chimpanzee. Further studies are necessary to develop an optimal protocol for the processing and cryopreservation of bonobo spermatozoa.
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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Allen KE, Greenbaum E, Hime PM, Tapondjou N. WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes. Ecol Evol 2021; 11:6133-6152. [PMID: 34141208 PMCID: PMC8207163 DOI: 10.1002/ece3.7429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.
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Affiliation(s)
- Kaitlin E. Allen
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Eli Greenbaum
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | - Paul M. Hime
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Walter P. Tapondjou N.
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Viktoria V. Sterkhova
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Chifundera Kusamba
- Laboratoire d’Hérpétologie, Département de BiologieCentre de Recherche en Sciences NaturellesLwiroDemocratic Republic of Congo
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Penner
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Chair of Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
| | - A. Townsend Peterson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
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Staes N, Guevara EE, Helsen P, Eens M, Stevens JMG. The Pan social brain: An evolutionary history of neurochemical receptor genes and their potential impact on sociocognitive differences. J Hum Evol 2021; 152:102949. [PMID: 33578304 DOI: 10.1016/j.jhevol.2021.102949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Humans have unique cognitive capacities that, compared with apes, are not only simply expressed as a higher level of general intelligence, but also as a quantitative difference in sociocognitive skills. Humans' closest living relatives, bonobos (Pan paniscus), and chimpanzees (Pan troglodytes), show key between-species differences in social cognition despite their close phylogenetic relatedness, with bonobos arguably showing greater similarities to humans. To better understand the evolution of these traits, we investigate the neurochemical mechanisms underlying sociocognitive skills by focusing on variation in genes encoding proteins with well-documented roles in mammalian social cognition: the receptors for vasopressin (AVPR1A), oxytocin (OXTR), serotonin (HTR1A), and dopamine (DRD2). Although these genes have been well studied in humans, little is known about variation in these genes that may underlie differences in social behavior and cognition in apes. We comparatively analyzed sequence data for 33 bonobos and 57 chimpanzees, together with orthologous sequence data for other apes. In all four genes, we describe genetic variants that alter the amino acid sequence of the respective receptors, raising the possibility that ligand binding or signal transduction may be impacted. Overall, bonobos show 57% more fixed substitutions than chimpanzees compared with the ancestral Pan lineage. Chimpanzees, show 31% more polymorphic coding variation, in line with their larger historical effective population size estimates and current wider distribution. An extensive literature review comparing allelic changes in Pan with known human behavioral variants revealed evidence of homologous evolution in bonobos and humans (OXTR rs4686301(T) and rs237897(A)), while humans and chimpanzees shared OXTR rs2228485(A), DRD2 rs6277(A), and DRD2 rs11214613(A) to the exclusion of bonobos. Our results offer the first in-depth comparison of neurochemical receptor gene variation in Pan and put forward new variants for future behavior-genotype association studies in apes, which can increase our understanding of the evolution of social cognition in modern humans.
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Affiliation(s)
- Nicky Staes
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium; Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 26, 2018, Antwerp, Belgium.
| | - Elaine E Guevara
- Evolutionary Anthropology, Duke University, 130 Science Dr, Durham, NC, 27708, USA
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 26, 2018, Antwerp, Belgium
| | - Marcel Eens
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Jeroen M G Stevens
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
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Giarla TC, Demos TC, Monadjem A, Hutterer R, Dalton D, Mamba ML, Roff EA, Mosher FM, Mikeš V, Kofron CP, Kerbis Peterhans JC. Integrative taxonomy and phylogeography of Colomys and Nilopegamys (Rodentia: Murinae), semi-aquatic mice of Africa, with descriptions of two new species. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The semi-aquatic African murine genera Colomys and Nilopegamys are considered monotypic and thought to be closely related to one another. Colomys occurs across forested regions of equatorial Africa, whereas Nilopegamys is known only from the Ethiopian holotype, making it among the rarest mammalian genera in the world – and possibly extinct. Using morphological and genetic data, we reassess the taxonomy of Colomys and Nilopegamys. A multilocus phylogeny with outgroups demonstrates that Nilopegamys is sister to Colomys. In addition, we recognize at least four morphologically diagnosable and genetically distinct species within Colomys: C. eisentrauti (elevated from subspecies and restricted to north-west Cameroon), C. goslingi (with a more restricted range than previously reported) and two new species (one from Liberia and Guinea and one from central and southern Democratic Republic of the Congo and Angola). We also review the status of four other taxa currently recognized within Colomys goslingi (bicolor, denti, goslingi and ruandensis) and demonstrate that these names lack phylogenetic and/or morphological support. Finally, we discuss potential biogeographic barriers that may have played a role in the evolution of Colomys and Nilopegamys, emphasizing the importance of rivers in both facilitating and, possibly, limiting dispersal within these genera.
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Affiliation(s)
| | - Terrence C Demos
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | | | - Desiré Dalton
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- South African National Biodiversity Institute, Pretoria, South Africa
| | - Mnqobi L Mamba
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Emily A Roff
- Department of Biology, Siena College, Loudonville, NY, USA
| | - Frank M Mosher
- Department of Biology, Siena College, Loudonville, NY, USA
| | - Václav Mikeš
- Museum of South Bohemia, České Budějovice, Czech Republic
| | | | - Julian C Kerbis Peterhans
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
- College of Arts and Sciences, Roosevelt University, Chicago, IL, USA
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12
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Van de Perre F, Willig MR, Presley SJ, Mukinzi IJC, Gambalemoke MS, Leirs H, Verheyen E. Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191582. [PMID: 32269793 PMCID: PMC7137932 DOI: 10.1098/rsos.191582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/22/2020] [Indexed: 06/11/2023]
Abstract
Understanding the determinants of species coexistence in complex and species-rich communities is a fundamental goal of ecology. Patterns of species coexistence depend on how biotic interactions and environmental filtering act over ecological and evolutionary time scales. Climatic fluctuations in lowland rainforests of the Congo Basin led to the number of vertebrate species being significantly lower in central compared with northern ecoregions of the Basin. We used null models to assess whether climatic variations affected the community assembly of shrews. A consistent limit to functional similarity of species was not related to species richness. Rather, species richness is constrained by environmental factors, and these constraints are stronger in the central lowland forests of the Congo Basin. By constraining species geographic distributions, historical effects of rainforest refugia arising from climatic fluctuations may affect contemporary species composition of local shrew communities. The Congo River represents a vicariance event that led to allopatric speciation of shrews and continues to represent a barrier to dispersal. Ultimately, the historical effects of this barrier have led to differences in the functional volume of shrew communities in northern and central ecoregions. We suggest that the analyses of community assembly can be used to identify Holocene refugia in the Congo Basin.
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Affiliation(s)
| | - Michael R. Willig
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & Engineering, and Institute of the Environment, University of Connecticut, Storrs, CT 06269-4210, USA
| | - Steven J. Presley
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & Engineering, and Institute of the Environment, University of Connecticut, Storrs, CT 06269-4210, USA
| | - Itoka Jean-Claude Mukinzi
- Centre de Surveillance de la Biodiversité, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Erik Verheyen
- Evolutionary Ecology Group, University of Antwerp, 2610 Antwerp, Belgium
- OD Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, 1000 Brussels, Belgium
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13
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van der Valk T, Gonda CM, Silegowa H, Almanza S, Sifuentes-Romero I, Hart TB, Hart JA, Detwiler KM, Guschanski K. The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets. Mol Biol Evol 2020; 37:183-194. [PMID: 31529046 PMCID: PMC6984364 DOI: 10.1093/molbev/msz213] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genomic data can be a powerful tool for inferring ecology, behavior, and conservation needs of highly elusive species, particularly, when other sources of information are hard to come by. Here, we focus on the Dryas monkey (Cercopithecus dryas), an endangered primate endemic to the Congo Basin with cryptic behavior and possibly <250 remaining adult individuals. Using whole-genome sequencing data, we show that the Dryas monkey represents a sister lineage to the vervets (Chlorocebus sp.) and has diverged from them ∼1.4 Ma with additional bidirectional gene flow ∼750,000–∼500,000 years ago that has likely involved the crossing of the Congo River. Together with evidence of gene flow across the Congo River in bonobos and okapis, our results suggest that the fluvial topology of the Congo River might have been more dynamic than previously recognized. Despite the presence of several homozygous loss-of-function mutations in genes associated with sperm mobility and immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individual. This suggests that the current population carries sufficient genetic variability for long-term survival and might be larger than currently recognized. We thus provide an example of how genomic data can directly improve our understanding of highly elusive species.
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Affiliation(s)
- Tom van der Valk
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Catalina M Gonda
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henri Silegowa
- Frankfurt Zoological Society, TL2 Project, Kinshasa, Democratic Republic of the Congo
| | - Sandra Almanza
- Department of Anthropology, Florida Atlantic University, Boca Raton, FL
| | | | - Terese B Hart
- Frankfurt Zoological Society, TL2 Project, Kinshasa, Democratic Republic of the Congo
| | - John A Hart
- Frankfurt Zoological Society, TL2 Project, Kinshasa, Democratic Republic of the Congo
| | - Kate M Detwiler
- Department of Anthropology, Florida Atlantic University, Boca Raton, FL.,Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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14
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Baden AL, Mancini AN, Federman S, Holmes SM, Johnson SE, Kamilar J, Louis EE, Bradley BJ. Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range. Sci Rep 2019; 9:16276. [PMID: 31700150 PMCID: PMC6838192 DOI: 10.1038/s41598-019-52689-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.
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Affiliation(s)
- Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
| | - Sarah Federman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Jason Kamilar
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, 01003, USA
| | - Edward E Louis
- Omaha's Henry Doorly Zoo and Aquarium, 3701S 10th St, Omaha, NE68107, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
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15
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Wang W, Zheng Y, Zhao J, Yao M. Low genetic diversity in a critically endangered primate: shallow evolutionary history or recent population bottleneck? BMC Evol Biol 2019; 19:134. [PMID: 31242851 PMCID: PMC6595580 DOI: 10.1186/s12862-019-1451-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current patterns of population genetic variation may have been shaped by long-term evolutionary history and contemporary demographic processes. Understanding the underlying mechanisms that yield those patterns is crucial for informed conservation of endangered species. The critically endangered white-headed langur, Trachypithecus leucocephalus, is endemic to a narrow range in southwest China. This species shows very low genetic diversity in its 2 main relict populations, Fusui and Chongzuo. Whether this has been caused by a short evolutionary history or recent population declines is unknown. Therefore, we investigated the contributions of historical and recent population demographic changes to population genetic diversity by using 15 nuclear microsatellite markers and mitochondrial DNA (mtDNA) control region sequences. RESULTS Using genetic data from 214 individuals we found a total of 9 mtDNA haplotypes in the Fusui population but only 1 haplotype in the Chongzuo population, and we found an overall low genetic diversity (haplotype and nucleotide diversities: h = 0.486 ± 0.036; π = 0.0028 ± 0.0003). The demographic history inferred from mtDNA and microsatellite markers revealed no evidence for historical population size fluctuations or recent population bottlenecks. Simulations of possible population divergence histories inferred by DIYABC analysis supported a recent divergence of the Chongzuo population from the Fusui population and no population bottlenecks. CONCLUSIONS Despite severe population declines caused by anthropogenic activities in the last century, the low genetic diversity of the extant white-headed langur populations is most likely primarily due to the species' shallow evolutionary history and to a recent, local population founder event.
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Affiliation(s)
- Weiran Wang
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China.,Beijing National Day School, Beijing, 100871, China
| | - Yitao Zheng
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing, 100871, China. .,Institute of Ecology, Peking University, Beijing, 100871, China.
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16
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Maibach V, Vigilant L. Reduced bonobo MHC class I diversity predicts a reduced viral peptide binding ability compared to chimpanzees. BMC Evol Biol 2019; 19:14. [PMID: 30630404 PMCID: PMC6327438 DOI: 10.1186/s12862-019-1352-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 01/02/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The highly polymorphic genes of the major histocompatibility complex (MHC) class I are involved in defense against viruses and other intracellular pathogens. Although several studies found reduced MHC class I diversity in bonobos in comparison to the closely related chimpanzee, it is unclear if this lower diversity also influences the functional ability of MHC class I molecules in bonobos. Here, we use a bioinformatic approach to analyze the viral peptide binding ability of all published bonobo MHC class I molecules (n = 58) in comparison to all published chimpanzee MHC class I molecules (n = 161) for the class I loci A, B, C and A-like. RESULTS We examined the peptide binding ability of all 219 different MHC class I molecules to 5,788,712 peptides derived from 1432 different primate viruses and analyzed the percentage of bound peptides and the overlap of the peptide binding repertoires of the two species. We conducted multiple levels of analysis on the "species"-, "population"- and "individual"-level to account for the characterization of MHC variation in a larger number of chimpanzees and their broader geographic distribution. We found a lower percentage of bound peptides in bonobos at the B locus in the "population"-level comparison and at the B and C loci in the "individual"-level comparison. Furthermore, we found evidence of a limited peptide binding repertoire in bonobos by tree-based visualization of functional clustering of MHC molecules, as well as an analysis of peptides bound by both species. CONCLUSION Our results suggest a reduced MHC class I viral peptide binding ability at the B and C loci in bonobos compared to chimpanzees. The effects of this finding on the immune defense against viruses in wild living bonobos are unclear. However, special caution is needed to prevent introduction and spread of new viruses to bonobos, as their defensive ability to cope with new viruses could be limited compared to chimpanzees.
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Affiliation(s)
- Vincent Maibach
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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17
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Serrano-Villavicencio JE, Hurtado CM, Vendramel RL, Nascimento FOD. Reconsidering the taxonomy of thePithecia irrorataspecies group (Primates: Pitheciidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyy167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- José Eduardo Serrano-Villavicencio
- Pós-graduação em Sistemática, Taxonomia Animal e Biodiversidade, Mastozoologia, Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré, 481, CEP 04263-000, Ipiranga, São Paulo, SP, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Perú
| | - Cindy M Hurtado
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Perú
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rafaela L Vendramel
- Pós-graduação em Sistemática, Taxonomia Animal e Biodiversidade, Mastozoologia, Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré, 481, CEP 04263-000, Ipiranga, São Paulo, SP, Brazil
| | - Fabio Oliveira do Nascimento
- Mastozoologia, Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, Ipiranga, São Paulo, SP, Brazil
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18
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Khanal L, Chalise MK, Wan T, Jiang X. Riverine barrier effects on population genetic structure of the Hanuman langur (Semnopithecus entellus) in the Nepal Himalaya. BMC Evol Biol 2018; 18:159. [PMID: 30382913 PMCID: PMC6211570 DOI: 10.1186/s12862-018-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/24/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Past climatological events and contemporary geophysical barriers shape the distribution, population genetic structure, and evolutionary history of many organisms. The Himalayan region, frequently referred to as the third pole of the Earth, has experienced large-scale climatic oscillations in the past and bears unique geographic, topographic, and climatic areas. The influences of the Pleistocene climatic fluctuations and present-day geographical barriers such as rivers in shaping the demographic history and population genetic structure of organisms in the Nepal Himalaya have not yet been documented. Hence, we examined the effects of late-Quaternary glacial-interglacial cycles and riverine barriers on the genetic composition of Hanuman langurs (Semnopithecus entellus), a colobine primate with a wide range of altitudinal distribution across the Nepalese Himalaya, using the mitochondrial DNA control region (CR, 1090 bp) and cytochrome B (CYTB, 1140 bp) sequences combined with paleodistribution modeling. RESULTS DNA sequences were successfully retrieved from 67 non-invasively collected fecal samples belonging to 18 wild Hanuman langur troops covering the entire distribution range of the species in Nepal. We identified 37 haplotypes from the concatenated CR + CYTB (2230 bp) sequences, with haplotype and nucleotide diversities of 0.958 ± 0.015 and 0.0237 ± 0.0008, respectively. The troops were clustered into six major clades corresponding to their river-isolated spatial distribution, with the significantly high genetic variation among these clades confirming the barrier effects of the snow-fed Himalayan rivers on genetic structuring. Analysis of demographic history projected a decrease in population size with the onset of the last glacial maximum (LGM); and, in accordance with the molecular analyses, paleodistribution modeling revealed a range shift in its suitable habitat downward/southward during the LGM. The complex genetic structure among the populations of central Nepal, and the stable optimal habitat through the last interglacial period to the present suggest that the central mid-hills of Nepal served as glacial refugia for the Hanuman langur. CONCLUSIONS Hanuman langurs of the Nepal Himalaya region exhibit high genetic diversity, with their population genetic structure is strongly shaped by riverine barrier effects beyond isolation by distance; hence, this species demands detailed future phylogenetic study.
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Affiliation(s)
- Laxman Khanal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223 China
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Mukesh Kumar Chalise
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
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19
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Sun Z, Wang H, Zhou W, Shi W, Zhu W, Zhang B. How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac ( Muntiacus reevesi)? DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Zhonglou Sun
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Hui Wang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenliang Zhou
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenbo Shi
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Weiquan Zhu
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Baowei Zhang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
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20
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Lo Bianco S, Masters JC, Sineo L. The evolution of the Cercopithecini: a (post)modern synthesis. Evol Anthropol 2017; 26:336-349. [PMID: 29265656 DOI: 10.1002/evan.21567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 11/11/2022]
Abstract
The Cercopithecini, or African guenon monkeys, are one of the most diverse clades of living primates and comprise the most species-rich clade of Catarrhini. Species identity is announced by flamboyant coloration of the facial and genital regions and, more cryptically, by vigorous chromosomal rearrangements among taxa. Beneath the skin, however, these animals are skeletally conservative and show low levels of genetic sequence divergence consonant with recent divergence between congeneric species. The guenons clearly demonstrate that morphological, cytogenetic, and reproductive differentiation proceed at different rates during speciation. We review diverse kinds of data in an effort to understand this conundrum.
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Affiliation(s)
- Stefania Lo Bianco
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 18, 90123, Palermo, Italy
| | - Judith C Masters
- African Primate Initiative for Ecology and Speciation (APIES), University of Fort Hare, and Africa Earth Observatory Network (AEON), Earth Stewardship Science Research Institute, Nelson Mandela University, 6031, Port Elizabeth, South Africa
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 18, 90123, Palermo, Italy
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21
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Liu W, Sherrill-Mix S, Learn GH, Scully EJ, Li Y, Avitto AN, Loy DE, Lauder AP, Sundararaman SA, Plenderleith LJ, Ndjango JBN, Georgiev AV, Ahuka-Mundeke S, Peeters M, Bertolani P, Dupain J, Garai C, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species. Nat Commun 2017; 8:1635. [PMID: 29158512 PMCID: PMC5696340 DOI: 10.1038/s41467-017-01798-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/16/2017] [Indexed: 02/01/2023] Open
Abstract
Malaria parasites, though widespread among wild chimpanzees and gorillas, have not been detected in bonobos. Here, we show that wild-living bonobos are endemically Plasmodium infected in the eastern-most part of their range. Testing 1556 faecal samples from 11 field sites, we identify high prevalence Laverania infections in the Tshuapa-Lomami-Lualaba (TL2) area, but not at other locations across the Congo. TL2 bonobos harbour P. gaboni, formerly only found in chimpanzees, as well as a potential new species, Plasmodium lomamiensis sp. nov. Rare co-infections with non-Laverania parasites were also observed. Phylogenetic relationships among Laverania species are consistent with co-divergence with their gorilla, chimpanzee and bonobo hosts, suggesting a timescale for their evolution. The absence of Plasmodium from most field sites could not be explained by parasite seasonality, nor by bonobo population structure, diet or gut microbiota. Thus, the geographic restriction of bonobo Plasmodium reflects still unidentified factors that likely influence parasite transmission.
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Affiliation(s)
- Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abigail P Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sesh A Sundararaman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012, Kisangani, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomedicale, University of Kinshasa, BP 1197, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier 1, BP 5045, Montpellier, 34394, France
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, CB2 1QH, UK
| | - Jef Dupain
- African Wildlife Foundation Conservation Centre, P.O. Box 310, 00502, Nairobi, Kenya
| | - Cintia Garai
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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22
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Ntie S, Davis AR, Hils K, Mickala P, Thomassen HA, Morgan K, Vanthomme H, Gonder MK, Anthony NM. Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba). BMC Evol Biol 2017; 17:212. [PMID: 28877669 PMCID: PMC5585889 DOI: 10.1186/s12862-017-1054-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/18/2017] [Indexed: 12/29/2022] Open
Abstract
Background This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Results Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Conclusions Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species’ capacity to adapt to environmental change. Electronic supplementary material The online version of this article (10.1186/s12862-017-1054-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephan Ntie
- Department of Biology, Université des Sciences et Techniques de Masuku, B.P.943, Franceville, Gabon.,Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Anne R Davis
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Katrin Hils
- Cheetah Conservation Fund, P.O. Box 1755, Otjiwarongo, Namibia.,Comparative Zoology, Institute for Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Patrick Mickala
- Department of Biology, Université des Sciences et Techniques de Masuku, B.P.943, Franceville, Gabon
| | - Henri A Thomassen
- Comparative Zoology, Institute for Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Katy Morgan
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Hadrien Vanthomme
- Département Ecologie et Gestion de la Biodiversité, Muséum National d'Histoire Naturelle, CNRS UMR 7179, Avenue du Petit Château, 91800, Brunoy, France
| | - Mary K Gonder
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Nicola M Anthony
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA.
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23
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Beaune D, Hohmann G, Serckx A, Sakamaki T, Narat V, Fruth B. How bonobo communities deal with tannin rich fruits: Re-ingestion and other feeding processes. Behav Processes 2017; 142:131-137. [DOI: 10.1016/j.beproc.2017.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
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24
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Takemoto H, Kawamoto Y, Higuchi S, Makinose E, Hart JA, Hart TB, Sakamaki T, Tokuyama N, Reinartz GE, Guislain P, Dupain J, Cobden AK, Mulavwa MN, Yangozene K, Darroze S, Devos C, Furuichi T. The mitochondrial ancestor of bonobos and the origin of their major haplogroups. PLoS One 2017; 12:e0174851. [PMID: 28467422 PMCID: PMC5414932 DOI: 10.1371/journal.pone.0174851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/16/2017] [Indexed: 11/28/2022] Open
Abstract
We report here where the most recent common ancestor (MRCA) of bonobos (Pan paniscus) ranged and how they dispersed throughout their current habitat. Mitochondrial DNA (mtDNA) molecular dating to analyze the time to MRCA (TMRCA) and the major mtDNA haplogroups of wild bonobos were performed using new estimations of divergence time of bonobos from other Pan species to investigate the dispersal routes of bonobos over the forest area of the Congo River’s left bank. The TMRCA of bonobos was estimated to be 0.64 or 0.95 million years ago (Ma). Six major haplogroups had very old origins of 0.38 Ma or older. The reconstruction of the ancestral area revealed the mitochondrial ancestor of the bonobo populations ranged in the eastern area of the current bonobos’ habitat. The haplogroups may have been formed from either the riparian forests along the Congo River or the center of the southern Congo Basin. Fragmentation of the forest refugia during the cooler periods may have greatly affected the formation of the genetic structure of bonobo populations.
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Affiliation(s)
- Hiroyuki Takemoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail: (HT); (TF)
| | - Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Shoko Higuchi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Emiko Makinose
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - John A. Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | - Térese B. Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | | | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Gay E. Reinartz
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Patrick Guislain
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Jef Dupain
- African Wildlife Foundation, Nairobi, Kenya
| | - Amy K. Cobden
- Department of Anthropology, Emory University, Atlanta, Georgia, United States of America
| | - Mbangi N. Mulavwa
- Research Center for Ecology and Forestry, Ministry of high Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Kumugo Yangozene
- Research Center for Ecology and Forestry, Ministry of high Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Serge Darroze
- Consultant Biodiversity, Sustainable Use of Natural Resources, Protected Areas Management and Adaptation to Climate Change, Bangkok, Thailand
| | - Céline Devos
- Department of Behavioral Biology, University of Liège, Liège, Belgium
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail: (HT); (TF)
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Wroblewski EE, Guethlein LA, Norman PJ, Li Y, Shaw CM, Han AS, Ndjango JBN, Ahuka-Mundeke S, Georgiev AV, Peeters M, Hahn BH, Parham P. Bonobos Maintain Immune System Diversity with Three Functional Types of MHC-B. THE JOURNAL OF IMMUNOLOGY 2017; 198:3480-3493. [PMID: 28348269 PMCID: PMC5469624 DOI: 10.4049/jimmunol.1601955] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
Abstract
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein. No Papa-B is identical to any chimpanzee Patr-B, human HLA-B, or gorilla Gogo-B. Phylogenetic analysis identified a clade of MHC-B, defined by residues 45-74 of the α1 domain, which is broadly conserved among bonobo, chimpanzee, and gorilla. Bonobo populations have 3-14 Papa-B allotypes. Three Papa-B are in all populations, and they are each of a different functional type: allotypes having the Bw4 epitope recognized by killer cell Ig-like receptors of NK cells, allotypes having the C1 epitope also recognized by killer cell Ig-like receptors, and allotypes having neither epitope. For population Malebo, these three Papa-B are the only Papa-B allotypes. Although small in number, their sequence divergence is such that the nucleotide diversity (mean proportional distance) of Papa-B in Malebo is greater than in the other populations and is also greater than expected for random combinations of three Papa-B Overall, Papa-B has substantially less diversity than Patr-B in chimpanzee subspecies and HLA-B in indigenous human populations, consistent with bonobo having experienced narrower population bottlenecks.
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Affiliation(s)
- Emily E Wroblewski
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alex S Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, 2012 Kisangani, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicales, 1197 Kinshasa, Democratic Republic of the Congo.,University of Kinshasa, 190 Kinshasa, Democratic Republic of the Congo.,Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Martine Peeters
- Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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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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27
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Sun Z, Pan T, Wang H, Pang M, Zhang B. Yangtze River, an insignificant genetic boundary in tufted deer ( Elaphodus cephalophus): the evidence from a first population genetics study. PeerJ 2016; 4:e2654. [PMID: 27843712 PMCID: PMC5103815 DOI: 10.7717/peerj.2654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/04/2016] [Indexed: 12/02/2022] Open
Abstract
Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Mujia Pang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.,School of Biosciences, Cardiff University, Cardiff, United Kingdom
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28
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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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29
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Beninde J, Feldmeier S, Werner M, Peroverde D, Schulte U, Hochkirch A, Veith M. Cityscape genetics: structural vs. functional connectivity of an urban lizard population. Mol Ecol 2016; 25:4984-5000. [DOI: 10.1111/mec.13810] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/23/2016] [Accepted: 07/19/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Joscha Beninde
- Department of Biogeography; Trier University; Universitätsring 15 54296 Trier Germany
| | - Stephan Feldmeier
- Department of Biogeography; Trier University; Universitätsring 15 54296 Trier Germany
| | - Maike Werner
- Zoological Institute & Museum; Ernst-Moritz-Arndt-Universität Greifswald; Johann Sebastian Bach-Str. 11/12 17487 Greifswald Germany
| | - Daniel Peroverde
- Department of Biogeography; Trier University; Universitätsring 15 54296 Trier Germany
| | - Ulrich Schulte
- Federal Agency for Nature Conservation (BfN); Konstantinstr. 110 53179 Bonn Germany
| | - Axel Hochkirch
- Department of Biogeography; Trier University; Universitätsring 15 54296 Trier Germany
| | - Michael Veith
- Department of Biogeography; Trier University; Universitätsring 15 54296 Trier Germany
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30
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Oshida T, Yasuda M, Sasaki M. Preliminary Study on Phylogeography ofCallosciurus prevostiiin Southeast Asia: Mitochondrial DNA Evidence Supports Riverine Barrier Hypothesis. MAMMAL STUDY 2016. [DOI: 10.3106/041.041.0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Vörös J, Mikulíček P, Major Á, Recuero E, Arntzen JW. Phylogeographic analysis reveals northerly refugia for the riverine amphibianTriturus dobrogicus(Caudata: Salamandridae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12866] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Judit Vörös
- Department of Zoology; Hungarian Natural History Museum; Baross u. 13. 1088 Budapest Hungary
- Molecular Taxonomy Laboratory; Hungarian Natural History Museum; Ludovika tér 2-6. 1083 Budapest Hungary
| | - Peter Mikulíček
- Department of Zoology; Faculty of Natural Sciences; Comenius University in Bratislava; Mlynská dolina Ilkovičova 6 SK-84215 Bratislava Slovak Republic
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic v.v.i.; Květná 8 CZ-60365 Brno Czech Republic
| | - Ágnes Major
- Molecular Taxonomy Laboratory; Hungarian Natural History Museum; Ludovika tér 2-6. 1083 Budapest Hungary
| | - Ernesto Recuero
- Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales MNCN-CSIC; C/José Gutiérrez Abascal, 2 28006 Madrid Spain
| | - Jan W. Arntzen
- Naturalis Biodiversity Center; P.O. BOX 9517 2300 RA Leiden the Netherlands
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32
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Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T. Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions. Genome Biol Evol 2016; 8:2020-30. [PMID: 27345955 PMCID: PMC4943195 DOI: 10.1093/gbe/evw124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 01/02/2023] Open
Abstract
The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.
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Affiliation(s)
- Irene Lobon
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Serena Tucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marc de Manuel
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | | | - Kiwoong Nam
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Mikkel H Schierup
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Aida M Andres
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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33
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Cullingham CI, Thiessen CD, Derocher AE, Paquet PC, Miller JM, Hamilton JA, Coltman DW. Population structure and dispersal of wolves in the Canadian Rocky Mountains. J Mammal 2016. [DOI: 10.1093/jmammal/gyw015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Meng S, Pan T, Sun Z, Bei Y, Meng T, Li G, Wu D, Zhang B. Extremely low genetic diversity of mtDNA control region and remarkable population differentiation of Ichthyophis bannanicus (Amphibia: Gymnophiona). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:98-103. [PMID: 26678840 DOI: 10.3109/19401736.2015.1110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It is widely accepted that the mitochondrial DNA (mtDNA) control region (CR) gene evolves more quickly than protein-encoding genes, such as ND2 and Cyt b, with few exceptions. However, some species have a different evolution pattern. In the present study, we sequenced the mtDNA CR partial sequences (454 base pairs) of 142 individuals from five sampling sites of Ichthyophis bannanicus and compared the genetic diversity and structure with the information from the NADH dehydrogenase subunit 2 (ND2) and Cytochrome b (Cyt b) genes within this species. Extremely low genetic diversity was found in the mtDNA CR compared with those of the ND2 and Cyt b genes. These results showed that the relatively mean clock rate of the CR was broadly lower than those of the ND2 (about 2.55 times) and Cyt b (about 3.14 times) genes. Despite the extremely low genetic diversity of CR, the population structure analysis identified two groups, Xishuangbanna and Northern Vietnam-Yulin-Yangchun-Deqing, which indicated that the Red River systems may have acted as gene-flow barriers for I. bannanicus.
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Affiliation(s)
- Shaoquan Meng
- a College of Life Sciences, Fujian Agriculture and Forest University , Fuzhou , Fujian , China.,b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Tao Pan
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
| | - Zhonglou Sun
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
| | - Yongjian Bei
- b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Tao Meng
- d Guangxi Forest Inventory and Planning Institute , Nanning , Guangxi , China
| | - Guifen Li
- b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Defeng Wu
- a College of Life Sciences, Fujian Agriculture and Forest University , Fuzhou , Fujian , China
| | - Baowei Zhang
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
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35
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Basabose AK, Inoue E, Kamungu S, Murhabale B, Akomo-Okoue EF, Yamagiwa J. Estimation of chimpanzee community size and genetic diversity in Kahuzi-Biega National Park, Democratic Republic of Congo. Am J Primatol 2015; 77:1015-1025. [PMID: 26118671 DOI: 10.1002/ajp.22435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 05/17/2015] [Accepted: 05/21/2015] [Indexed: 11/11/2022]
Abstract
A small chimpanzee habitat in the montane forest of Kahuzi-Biega National Park, Democratic Republic of Congo, is connected with the lowland forest of this park through a corridor, which is affected by human encroachment. To assess the conservation status of the chimpanzee population in this small habitat, we estimated the size of the community and evaluated its genetic diversity by using 279 fecal samples collected in the montane forest of Kahuzi. Using autosomal microsatellite (or short tandem repeat, STR) loci, we identified 32 individuals, comprising 19 females and 13 males. Samples from 24 individuals were collected at least twice and a genetic mark-recapture analysis estimated that the community size was 36 (range: 32-42). Data on nest site sharing confirmed that all the samples belonged to the same community. Nest site sharing information may be useful in population studies of unhabituated chimpanzees. The genetic structure and diversity of the 32 genotyped individuals was assessed using Y-chromosomal short tandem repeat (Y-STR) loci and mitochondrial D-loops. One dominant Y-STR haplotype was found, whereas there was no dominant haplotype in the mitochondrial region, reflecting a female-biased dispersal pattern, which is typical of chimpanzees. The genetic diversity for three markers in Kahuzi chimpanzees was comparable to that in other eastern chimpanzee populations. A relatively high heterozygosity and negative inbreeding coefficient (FIS ) for STR loci suggests that the study community belongs to an outbreeding chimpanzee population. These findings suggest that individuals of the study community may have reproductive contact with other chimpanzee individuals from neighboring communities in Kahuzi-Biega National Park, at least in the recent past. Am. J. Primatol. 77:1015-1025, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Augustin K Basabose
- Laboratoire de Primatologie, Centre de Recherche en Science Naturelles de Lwiro, Democratic Republic of Congo
| | - Eiji Inoue
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Sebulimbwa Kamungu
- Laboratoire de Primatologie, Centre de Recherche en Science Naturelles de Lwiro, Democratic Republic of Congo
| | - Bertin Murhabale
- Laboratoire de Primatologie, Centre de Recherche en Science Naturelles de Lwiro, Democratic Republic of Congo
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36
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Link A, Valencia LM, Céspedes LN, Duque LD, Cadena CD, Di Fiore A. Phylogeography of the Critically Endangered Brown Spider Monkey (Ateles hybridus): Testing the Riverine Barrier Hypothesis. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9840-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Wang H, Luo X, Meng S, Bei Y, Song T, Meng T, Li G, Zhang B. The Phylogeography and Population Demography of the Yunnan Caecilian (Ichthyophis bannanicus): Massive Rivers as Barriers to Gene Flow. PLoS One 2015; 10:e0125770. [PMID: 25915933 PMCID: PMC4411157 DOI: 10.1371/journal.pone.0125770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/26/2015] [Indexed: 11/23/2022] Open
Abstract
Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15–17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.
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Affiliation(s)
- Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xia Luo
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Shaoquan Meng
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Yongjian Bei
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
| | - Tao Song
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forestry Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Guifen Li
- College of Life Science & Technology, Yulin Normal University, Yulin, 537000, Guangxi, China
- * E-mail: (GL); (BZ)
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- * E-mail: (GL); (BZ)
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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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Stanton DWG, Hart J, Galbusera P, Helsen P, Shephard J, Kümpel NF, Wang J, Ewen JG, Bruford MW. Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni). PLoS One 2014; 9:e101081. [PMID: 25007188 PMCID: PMC4090074 DOI: 10.1371/journal.pone.0101081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/02/2014] [Indexed: 11/22/2022] Open
Abstract
The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.
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Affiliation(s)
| | - John Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | - Peter Galbusera
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jill Shephard
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Noëlle F. Kümpel
- Conservation Programmes, Zoological Society of London, London, United Kingdom
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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Fünfstück T, Arandjelovic M, Morgan DB, Sanz C, Breuer T, Stokes EJ, Reed P, Olson SH, Cameron K, Ondzie A, Peeters M, Kühl HS, Cipolletta C, Todd A, Masi S, Doran-Sheehy DM, Bradley BJ, Vigilant L. The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest. Am J Primatol 2014; 76:868-78. [PMID: 24700547 DOI: 10.1002/ajp.22274] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/18/2013] [Accepted: 02/10/2014] [Indexed: 11/07/2022]
Abstract
To understand the evolutionary histories and conservation potential of wild animal species it is useful to assess whether taxa are genetically structured into different populations and identify the underlying factors responsible for any clustering. Landscape features such as rivers may influence genetic population structure, and analysis of structure by sex can further reveal effects of sex-specific dispersal. Using microsatellite genotypes obtained from noninvasively collected fecal samples we investigated the population structure of 261 western lowland gorillas (WLGs) (Gorilla gorilla gorilla) from seven locations spanning an approximately 37,000 km(2) region of mainly continuous rain forest within Central African Republic (CAR), Republic of Congo and Cameroon. We found our sample to consist of two or three significantly differentiated clusters. The boundaries of the clusters coincided with courses of major rivers. Moreover, geographic distance detoured around rivers better-explained variation in genetic distance than straight line distance. Together these results suggest that major rivers in our study area play an important role in directing WLG gene flow. The number of clusters did not change when males and females were analyzed separately, indicating a lack of greater philopatry in WLG females than males at this scale.
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Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Sabin R, Werdelin L, Cuisin J, Larson G. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol 2014; 14:70. [PMID: 24690312 PMCID: PMC3997813 DOI: 10.1186/1471-2148-14-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. Results We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. Conclusions We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
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Affiliation(s)
- Ross Barnett
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK.
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Phiri EE, Daniels SR. Disentangling the divergence and cladogenesis in the freshwater crab species (Potamonautidae:Potamonautes perlatus sensu lato) in the Cape Fold Mountains, South Africa, with the description of two novel cryptic lineages. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ethel E. Phiri
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Savel R. Daniels
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
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Pilbrow V, Groves C. Evidence for Divergence in Populations of Bonobos (Pan paniscus) in the Lomami-Lualaba and Kasai-Sankuru Regions Based on Preliminary Analysis of Craniodental Variation. INT J PRIMATOL 2013. [DOI: 10.1007/s10764-013-9737-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hvilsom C, Carlsen F, Heller R, Jaffré N, Siegismund HR. Contrasting demographic histories of the neighboring bonobo and chimpanzee. Primates 2013; 55:101-12. [DOI: 10.1007/s10329-013-0373-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/10/2013] [Indexed: 12/01/2022]
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Kawamoto Y, Takemoto H, Higuchi S, Sakamaki T, Hart JA, Hart TB, Tokuyama N, Reinartz GE, Guislain P, Dupain J, Cobden AK, Mulavwa MN, Yangozene K, Darroze S, Devos C, Furuichi T. Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution. PLoS One 2013; 8:e59660. [PMID: 23544084 PMCID: PMC3609822 DOI: 10.1371/journal.pone.0059660] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/16/2013] [Indexed: 11/18/2022] Open
Abstract
Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.
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Affiliation(s)
- Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Shoko Higuchi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - John A. Hart
- Lukuru Wildlife Research Foundation, Kinshasa, Democratic Republic of Congo
| | - Terese B. Hart
- Lukuru Wildlife Research Foundation, Kinshasa, Democratic Republic of Congo
| | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Gay E. Reinartz
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Patrick Guislain
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Jef Dupain
- African Wildlife Foundation, Kinshasa, Democratic Republic of Congo
| | - Amy K. Cobden
- African Wildlife Foundation, Kinshasa, Democratic Republic of Congo
- Department of Anthropology, Emory University, Atlanta, Georgia, United States of America
| | - Mbangi N. Mulavwa
- Research Center for Ecology and Forestry, Ministry of High Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Kumugo Yangozene
- Research Center for Ecology and Forestry, Ministry of High Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Serge Darroze
- World Wide Fund for Nature, Kinshasa, Democratic Republic of Congo
| | - Céline Devos
- World Wide Fund for Nature, Kinshasa, Democratic Republic of Congo
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail:
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Piel AK, Stewart FA, Pintea L, Li Y, Ramirez MA, Loy DE, Crystal PA, Learn GH, Knapp LA, Sharp PM, Hahn BH. The malagarasi river does not form an absolute barrier to chimpanzee movement in Western Tanzania. PLoS One 2013; 8:e58965. [PMID: 23536841 PMCID: PMC3594223 DOI: 10.1371/journal.pone.0058965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Malagarasi River has long been thought to be a barrier to chimpanzee movements in western Tanzania. This potential geographic boundary could affect chimpanzee ranging behavior, population connectivity and pathogen transmission, and thus has implications for conservation strategies and government policy. Indeed, based on mitochondrial DNA sequence comparisons it was recently argued that chimpanzees from communities to the north and to the south of the Malagarasi are surprisingly distantly related, suggesting that the river prevents gene flow. To investigate this, we conducted a survey along the Malagarasi River. We found a ford comprised of rocks that researchers could cross on foot. On a trail leading to this ford, we collected 13 fresh fecal samples containing chimpanzee DNA, two of which tested positive for SIVcpz. We also found chimpanzee feces within the riverbed. Taken together, this evidence suggests that the Malagarasi River is not an absolute barrier to chimpanzee movements and communities from the areas to the north and south should be considered a single population. These results have important consequences for our understanding of gene flow, disease dynamics and conservation management.
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Affiliation(s)
- Alex K Piel
- Department of Anthropology, University of California San Diego, San Diego, California, United States of America.
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Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence. PLoS One 2013; 8:e56235. [PMID: 23437100 PMCID: PMC3578844 DOI: 10.1371/journal.pone.0056235] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
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Inoue E, Tashiro Y, Ogawa H, Inoue-Murayama M, Nishida T, Takenaka O. Gene Flow and Genetic Diversity of Chimpanzees in Tanzanian Habitats. ACTA ACUST UNITED AC 2013. [DOI: 10.1896/052.026.0105] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Minhós T, Nixon E, Sousa C, Vicente LM, da Silva MF, Sá R, Bruford MW. Genetic evidence for spatio-temporal changes in the dispersal patterns of two sympatric African colobine monkeys. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:464-74. [DOI: 10.1002/ajpa.22223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 12/05/2012] [Indexed: 11/09/2022]
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