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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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2
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Blair ME, Cao GTH, López-Nandam EH, Veronese-Paniagua DA, Birchette MG, Kenyon M, Md-Zain BM, Munds RA, Nekaris KAI, Nijman V, Roos C, Thach HM, Sterling EJ, Le MD. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius. Genes (Basel) 2023; 14:643. [PMID: 36980915 PMCID: PMC10048081 DOI: 10.3390/genes14030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.
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Affiliation(s)
- Mary E. Blair
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Giang T. H. Cao
- Department of Genetics, Vietnam National University, Hanoi 10000, Vietnam
| | - Elora H. López-Nandam
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Institute for Biodiversity and Sustainability Science, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Daniel A. Veronese-Paniagua
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- The Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mark G. Birchette
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Department of Biology, Long Island University Brooklyn, Brooklyn, NY 11201, USA
| | - Marina Kenyon
- Dao Tien Endangered Primate Species Centre, Dong Nai 76000, Vietnam
| | - Badrul M. Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi Selangor 43600, Malaysia
| | - Rachel A. Munds
- Department of Anthropology & Archeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Vincent Nijman
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Hoàng M. Thach
- Department of Anthropology, Vietnam National University, Hanoi 10000, Vietnam
- Department of Geography & Human Ecology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Eleanor J. Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Minh D. Le
- Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 10000, Vietnam
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3
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Penna A, Dillon R, Bearder SK, Karlsson J, Perkin A, Pozzi L. Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.
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Affiliation(s)
- Anna Penna
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Rosemarie Dillon
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
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4
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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5
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Nekaris KAI, Nijman V. A new genus name for pygmy lorises, Xanthonycticebus gen. nov. (Mammalia, primates). ZOOSYST EVOL 2022. [DOI: 10.3897/zse.98.81942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lorisiformes are nocturnal primates from Africa and Asia with four genera, with two (Arctocebus and Loris), three (Perodicticus) and nine (Nycticebus) recognised species. Their cryptic lifestyle and lack of study have resulted in an underappreciation of the variation at the species and genus level. There are marked differences between the pygmy slow loris Nycticebus pygmaeus and the other Nycticebus species and, in the past, several authors have suggested that these may warrant recognition at the generic level. We here combine morphological, behavioural, karyotypical and genetic data to show that these contrasts are, indeed, significantly large and consistent. We propose Xanthonycticebus gen. nov. as a new genus name for the pygmy slow lorises and suggest a common name of pygmy lorises. Based on analysis of complete mitochondrial DNA sequences, we calculate the divergence of pygmy from slow lorises at 9.9–10.0%. The median date, calculated for the divergence between Xanthonycticebus and Nycticebus, is 10.5 Mya (range 4.9–21.0 Mya). Xanthonycticebus differs from Nycticebus by showing sympatry with other slow loris species, by habitually giving birth to twins, by showing seasonal body mass and whole body coat colour changes (absent in other species living at similar latitudes) and a multi-male, multi-female social system. Pygmy lorises are easily recognisable by the absence of hair on their ears and more protruding premaxilla. Xanthonycticebus is threatened by habitat loss and illegal trade despite legal protection across their range and all slow lorises are listed on appendix 1 of CITES. The suggested nomenclatural changes should not affect their legal status.
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6
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Munds RA, Titus CL, Moreira LAA, Eggert LS, Blomquist GE. Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae). Ecol Evol 2021; 11:4442-4459. [PMID: 33976821 PMCID: PMC8093732 DOI: 10.1002/ece3.7338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023] Open
Abstract
Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
- Nocturnal Primate Research GroupOxford Brookes UniversityOxfordUK
| | - Chelsea L. Titus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Lais A. A. Moreira
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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7
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Vocalization Analyses of Nocturnal Arboreal Mammals of the Taita Hills, Kenya. DIVERSITY 2020. [DOI: 10.3390/d12120473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Three poorly known nocturnal mammal species from the montane forests of the Taita Hills in Kenya, were studied via vocalization analysis. Here, their acoustic behaviour is described. The studied animals were the tree hyrax (Dendrohyrax sp.), the small-eared greater galago (Otolemur garnettii), and the dwarf galago (Paragalago sp.). High-quality loud calls were analysed using RAVEN PRO, and compared to calls of presumed closest relatives. Our findings include the first detailed descriptions of tree hyrax songs. Moreover, our results suggest that the tree hyrax of Taita Hills may be a taxon new to science, as it produces a characteristic call, the ‘strangled thwack’, not previously known from other Dendrohyrax populations. Our data confirms that the small-eared greater galago subspecies living in the Taita Hills is Otolemur garnettii lasiotis. The loud calls of the elusive Taita Hills dwarf galago closely resemble those of the Kenya coast dwarf galago (Paragalago cocos). Thus, the population in the Taita Hills probably belongs to this species. The Taita Hills dwarf galagos are geographically isolated from other dwarf galago populations, and live in montane cloud forest, which is an unusual habitat for P. cocos. Intriguingly, two dwarf galago subpopulations living in separate forest patches in the Taita Hills, Ngangao and Mbololo, have clearly different contact calls. The Paragalagos in Mbololo Forest may represent a population of P. cocos with a derived call repertoire, or, alternatively, they may actually be mountain dwarf galagos (P. orinus). Hence, differences in habitat, behaviour, and contact call structure suggest that there may be two different Paragalago species in the montane forests of the Taita Hills.
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8
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Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues. mBio 2020; 11:mBio.02772-20. [PMID: 33203760 PMCID: PMC7683403 DOI: 10.1128/mbio.02772-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Organisms can access genetic and functional novelty by capturing viral elements within their genomes, where they can evolve to drive new cellular or organismal processes. We demonstrate that a retroviral envelope gene, EnvP(b)1, has been maintained and its fusion activity preserved for 40 to 71 million years. It is expressed as a protein in multiple healthy human tissues. We determined the structure of its inferred receptor binding domain and compared it with the same domain in modern viruses. We found a common conserved architecture that underlies the varied receptor binding activity of divergent Env genes. The modularity and versatility of this domain may underpin the evolutionary success of this clade of fusogens. EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.
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9
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Lemarcis T, Chesnais CB, Pion SDS, Boussinesq M, Locatelli S. Detection of a Larva of Armillifer armillatus in a Potto (Perodicticus potto) from the Republic of the Congo. J Parasitol 2020; 106:654-662. [PMID: 33079999 DOI: 10.1645/20-51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We determined the complete sequence of the mitochondrial DNA (mtDNA) of a parasite discovered between the subcutaneous tissue and the peritoneum of an African nocturnal non-human primate (NHP). The parasite and host sequences were obtained by a combination of Sanger sequencing and nanopore MinION techniques. Analyses of mtDNA gene arrangements and sequences unambiguously showed that the parasite investigated was the pentastomid Armillifer armillatus, also commonly named the tongue worm. The full-length mitochondrial genome of A. armillatus, measuring 16,706 bp in length, contains 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, an arrangement identical to that of previously described pentastomid mitochondrial genomes. We describe here the second full mitochondrial genome of A. armillatus to date. To identify the NHP host, maximum likelihood phylogenetic analyses of a 441-bp fragment on the 12S rDNA gene and of a 1,140-bp fragment of the mitochondrial cytochrome b strongly support clustering with the African lorisid Perodicticus potto, a species that has rarely been reported as an intermediate host of this parasite.
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Affiliation(s)
- Thomas Lemarcis
- IRD, UMI 233-TransVIHMI-INSERM U1175, University de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Cédric Benjamin Chesnais
- IRD, UMI 233-TransVIHMI-INSERM U1175, University de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Sébastien David Serge Pion
- IRD, UMI 233-TransVIHMI-INSERM U1175, University de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Michel Boussinesq
- IRD, UMI 233-TransVIHMI-INSERM U1175, University de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Sabrina Locatelli
- IRD, UMI 233-TransVIHMI-INSERM U1175, University de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,Current address: IRD, UMR 224-CNRS5290-MIVEGEC, University de Montpellier, MIVEGEC, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
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10
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Pozzi L, Penna A, Bearder SK, Karlsson J, Perkin A, Disotell TR. Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex. Mol Phylogenet Evol 2020; 150:106887. [PMID: 32534184 DOI: 10.1016/j.ympev.2020.106887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/04/2020] [Accepted: 06/03/2020] [Indexed: 11/17/2022]
Abstract
The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Todd R Disotell
- Department of Anthropology, New York University, New York, NY, USA; Department of Anthropology, University of Massachusetts, Amherst, MA, USA
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11
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Frias L, Hasegawa H, Stark DJ, Lynn MS, Nathan SK, Chua TH, Goossens B, Okamoto M, MacIntosh AJJ. A pinworm's tale: The evolutionary history of Lemuricola (Protenterobius) nycticebi. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 8:25-32. [PMID: 30619706 PMCID: PMC6299129 DOI: 10.1016/j.ijppaw.2018.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022]
Abstract
Lemuricola (Protenterobius) nycticebi is the only pinworm species known to infect strepsirrhine primates outside Africa, and the only pinworm species yet described in slow lorises. Here, we provided a detailed morphological comparison of female and male worms, and a first description of fourth-stage larvae collected from free-living slow lorises (Nycticebus menagensis) in Sabah, Malaysian Borneo. Using mitochondrial and nuclear markers, we also reconstructed the species' phylogenetic relationship with other pinworms infecting primates. Both morphological and molecular results indicated a distinct association between L. (P.) nycticebi and its host. However, while taxonomy identified this species as a member of the Lemuricola clade and grouped pinworms infecting lemurs and slow lorises together, phylogenetic reconstruction split them, placing L. (P.) nycticebi within the Enterobius clade. Our results suggest that L. (P.) nycticebi may represent a different taxon altogether, and that it is more closely related to pinworm species infecting Old World primates outside Madagascar. Pongobius pongoi (Foitová et al., 2008) n. comb. is also proposed. Pinworms and their primate hosts have a long history of association. L. (P.) nycticebi was recovered from slow lorises in the wild. L. (P.) nycticebi was taxonomy classified within the Lemuricola clade. However, molecular phylogenetics placed it within the Enterobius clade. Taxonomic and molecular identifications should complement species descriptions.
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Affiliation(s)
- Liesbeth Frias
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hideo Hasegawa
- Department of Biomedicine and Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Danica J Stark
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia
| | - Milena Salgado Lynn
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia.,Wildlife Health, Genetic and Forensic Laboratory, Kota Kinabalu, Sabah, Malaysia.,Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | | | - Tock H Chua
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Benoit Goossens
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia.,Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia.,Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | | | - Andrew J J MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan.,Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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12
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Luhrs AM, Svensson MS, Nekaris KAI. Comparative Ecology and Behaviour of Eastern Potto Perodicticus ibeanus and Central Potto P. Edwardsi in Angola, Cameroon, Kenya, Nigeria, Rwanda and Uganda. ACTA ACUST UNITED AC 2018. [DOI: 10.2982/028.107.0104] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Averee M. Luhrs
- Nocturnal Primate Research Group, Oxford Brookes University Headington, Oxford, OX3 0BP, UK
| | - Magdalena S. Svensson
- Nocturnal Primate Research Group, Oxford Brookes University Headington, Oxford, OX3 0BP, UK
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Oxford Brookes University Headington, Oxford, OX3 0BP, UK
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13
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Blanco MB, Dausmann KH, Faherty SL, Yoder AD. Tropical heterothermy is “cool”: The expression of daily torpor and hibernation in primates. Evol Anthropol 2018; 27:147-161. [DOI: 10.1002/evan.21588] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/15/2018] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | - Anne D. Yoder
- Duke Lemur Center; Durham North Carolina
- Department of Biology; Duke University; Durham North Carolina
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Sleep patterns, daytime predation, and the evolution of diurnal sleep site selection in lorisiforms. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:563-577. [DOI: 10.1002/ajpa.23450] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 02/02/2018] [Accepted: 02/15/2018] [Indexed: 12/30/2022]
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15
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McKenney EA, Maslanka M, Rodrigo A, Yoder AD. Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes. MICROBIAL ECOLOGY 2018; 76:272-284. [PMID: 29188302 DOI: 10.1007/s00248-017-1114-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/20/2017] [Indexed: 05/25/2023]
Abstract
Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists-the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls-the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.029) compared to both the giant panda (8.256; p = 0.0001936) and the red panda (6.484; p = 0.0000029). We also detected significantly enriched bacterial taxa that distinguished each species. Our results complement previous work in finding that phylogeny predominantly governs high-level microbiome community structure. However, we also find that 48 low-abundance OTUs are shared among bamboo specialists, compared to only 8 OTUs shared by the bamboo lemur and its sister species, the ringtail lemur (Lemur catta, a generalist). Our results suggest that deep sequencing is necessary to detect low-abundance bacterial OTUs, which may be specifically adapted to a high-fiber diet. These findings provide a more comprehensive framework for understanding the evolution and ecology of the microbiome as well as the host.
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Affiliation(s)
- Erin A McKenney
- Department of Biology, Duke University, Durham, NC, USA.
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.
| | - Michael Maslanka
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, USA
| | - Allen Rodrigo
- Department of Biology, Duke University, Durham, NC, USA
- Australia National University, Canberra, Australia
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
- Duke Lemur Center, Duke University, Durham, NC, USA
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16
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Munds RA, Titus CL, Eggert LS, Blomquist GE. Using a multi-gene approach to infer the complicated phylogeny and evolutionary history of lorises (Order Primates: Family Lorisidae). Mol Phylogenet Evol 2018; 127:556-567. [PMID: 29807155 DOI: 10.1016/j.ympev.2018.05.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/19/2018] [Accepted: 05/18/2018] [Indexed: 11/25/2022]
Abstract
Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya (Perelman et al., 2011; Pozzi et al., 2014). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.
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Affiliation(s)
- Rachel A Munds
- Department of Anthropology, University of Missouri, Columbia, MO 65211, United States; Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
| | - Chelsea L Titus
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Lori S Eggert
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Gregory E Blomquist
- Department of Anthropology, University of Missouri, Columbia, MO 65211, United States
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17
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Dagosto M, Gebo D, Ni X, Smith T. Estimating body size in early primates: The case of Archicebus and Teilhardina. J Hum Evol 2018; 115:8-19. [DOI: 10.1016/j.jhevol.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/26/2016] [Accepted: 02/20/2017] [Indexed: 01/08/2023]
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18
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Kunimatsu Y, Nakatsukasa M, Sakai T, Saneyoshi M, Sawada Y, Nakaya H. A newly discovered galagid fossil from Nakali, an early Late Miocene locality of East Africa. J Hum Evol 2017; 105:123-126. [PMID: 28318607 DOI: 10.1016/j.jhevol.2017.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Yutaka Kunimatsu
- Faculty of Business Administration, Ryukoku University, Fushimi, Kyoto, 612-8577, Japan.
| | - Masato Nakatsukasa
- Laboratory of Physical Anthropology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
| | - Tetsuya Sakai
- Department of Geoscience, Faculty of Science and Engineering, Shimane University, Matsue, Shimane, 690-8504, Japan.
| | - Mototaka Saneyoshi
- Faculty of Biosphere-Geosphere Science, Okayama University of Science, Okayama, 700-0005, Japan.
| | - Yoshihiro Sawada
- Professor Emeritus, Shimane University, Matsue, Shimane, 690-8504, Japan.
| | - Hideo Nakaya
- Department of Earth and Environmental Science, Faculty of Science, Kagoshima University, Korimoto 1-21-35, Kagoshima, 890-0065, Japan.
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Svensson MS, Bersacola E, Mills MSL, Munds RA, Nijman V, Perkin A, Masters JC, Couette S, Nekaris KAI, Bearder SK. A giant among dwarfs: a new species of galago (Primates: Galagidae) from Angola. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:30-43. [DOI: 10.1002/ajpa.23175] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/01/2017] [Accepted: 01/02/2017] [Indexed: 11/08/2022]
Affiliation(s)
| | - Elena Bersacola
- Nocturnal Primate Research Group; Oxford Brookes University; Oxford OX3 0BP UK
| | - Michael S. L. Mills
- A. P. Leventis Ornithological Research Institute; University of Jos; Jos 930001 Nigeria
| | - Rachel A. Munds
- Department of Anthropology; University of Missouri Columbia; Columbia Missouri 65211
| | - Vincent Nijman
- Nocturnal Primate Research Group; Oxford Brookes University; Oxford OX3 0BP UK
| | - Andrew Perkin
- Nocturnal Primate Research Group; Oxford Brookes University; Oxford OX3 0BP UK
- Tanzania Forest Conservation Group; Dar es Salaam Tanzania
| | - Judith C. Masters
- African Primate Initiative for Ecology and Speciation, Africa Earth Observatory Network, Earth Stewardship Science Research Institute; Nelson Mandela Metropolitan University; Port Elizabeth 6031 South Africa
| | - Sébastien Couette
- EPHE, PSL Research University, Paris, France & UMR CNRS 6282 “Biogéosciences”, Univ. Bourgogne Franche-Comté; Dijon 21000 France
| | | | - Simon K. Bearder
- Nocturnal Primate Research Group; Oxford Brookes University; Oxford OX3 0BP UK
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Masters JC, Génin F, Couette S, Groves CP, Nash SD, Delpero M, Pozzi L. A new genus for the eastern dwarf galagos (Primates: Galagidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw028] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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Génin F, Yokwana A, Kom N, Couette S, Dieuleveut T, Nash SD, Masters JC. A new galago species for South Africa (Primates: Strepsirhini: Galagidae). AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1232602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Fabien Génin
- African Primate Initiative for Ecology and Speciation, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Ayabulela Yokwana
- African Primate Initiative for Ecology and Speciation, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Nokuthula Kom
- African Primate Initiative for Ecology and Speciation, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Sébastien Couette
- Ecole Pratique des Hautes Etudes, Laboratoire Paléobiodiversité et Evolution and UMR uB CNRS 6282 “Biogéosciences”, Université de Bourgogne, Dijon, France
| | | | | | - Judith C Masters
- African Primate Initiative for Ecology and Speciation, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
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23
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Niche partitioning and environmental factors affecting abundance of strepsirrhines in Angola. Am J Primatol 2015; 77:1179-92. [DOI: 10.1002/ajp.22457] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/28/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022]
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24
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Masters JC, Couette S. Characterizing cryptic species: A morphometric analysis of craniodental characters in the dwarf galago genusGalagoides. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:288-299. [DOI: 10.1002/ajpa.22792] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/28/2015] [Accepted: 05/28/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Judith C. Masters
- African Primate Initiative for Ecology and Speciation; Department of Zoology and Entomology; University of Fort Hare; Private Bag X1314 Alice 5700 South Africa
| | - Sébastien Couette
- Ecole Pratique des Hautes Etudes; Laboratoire Paléobiodiversité et Evolution & UMR uB CNRS 6282 «Biogéosciences»; Université de Bourgogne; 6 Bld Gabriel Dijon 21000 France
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