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Halajian A, Cuozzo FP, Heyne H, Sauther ML, Linden B, Linden J, Tordiffe AS, Rampedi KM, Hornok S. Hard ticks (Acari: Ixodidae) parasitizing bushbabies (Mammalia: Galagidae) in a biodiversity hotspot of northern South Africa. Ticks Tick Borne Dis 2024; 15:102313. [PMID: 38278012 DOI: 10.1016/j.ttbdis.2024.102313] [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: 11/07/2023] [Revised: 01/07/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
South Africa has six species of primates, three of which are bushbabies (family Galagidae). Very little information is available on their parasites due to the lack of longitudinal studies, although Rhipicephalus appendiculatus, Amblyomma hebraeum and Haemaphysalis elliptica were previously reported from the brown greater galago (Otolemur crassicaudatus) in South Africa. During 2014-2019, 83 O. crassicaudatus (70 live-trapped and 13 deceased animals) were checked for the presence of hard ticks, all from Limpopo Province, South Africa. Seventy-three of 83 (88 %) galagos were found to be tick-infested. Among ixodid genera, Haemaphysalis had the highest prevalence (46 % of the bushbabies), followed by Rhipicephalus (25 %) and Ixodes (18 %). In total, ten tick species were identified. Importantly, all infestations were monospecific. Ticks occurred on various body parts of bushbabies, thus no predilection site was noted. In conclusion, while previously only three ixodid species were known to infest bushbabies in South Africa, the present study showed that these animals can be parasitized by a much broader range of hard ticks.
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Affiliation(s)
- Ali Halajian
- Research Administration and Development, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa.
| | - Frank P Cuozzo
- Mammal Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Heloise Heyne
- 3 Kappertjie Crescent, Doornpoort, Pretoria 0186 South Africa
| | - Michelle L Sauther
- Department of Anthropology, University of Colorado, Campus Box 233, Boulder, CO 80509, United States
| | - Birthe Linden
- SARChI Chair on Biodiversity Value and Change, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950 South Africa
| | - Jabu Linden
- P. O. Box 1536 Louis Trichardt Makhado, South Africa
| | - Adrian Sw Tordiffe
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa; Department of Research and Scientific Services, National Zoological Gardens of South Africa, Pretoria, South Africa; Centre for Human Metabolomics, Faculty of Natural Sciences, North-West University, Potchefstroom, South Africa
| | | | - Sándor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, 1078 Budapest, Hungary; HUN-REN-UVMB Climate Change: New Blood-sucking Parasites and Vector-borne Pathogens Research Group, 1078 Budapest, Hungary.
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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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Douglas J, Bouckaert R. Quantitatively defining species boundaries with more efficiency and more biological realism. Commun Biol 2022; 5:755. [PMID: 35902726 PMCID: PMC9334598 DOI: 10.1038/s42003-022-03723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
We introduce a widely applicable species delimitation method based on the multispecies coalescent model that is more efficient and more biologically realistic than existing methods. We extend a threshold-based method to allow the ancestral speciation rate to vary through time as a smooth piecewise function. Furthermore, we introduce the cutting-edge proposal kernels of StarBeast3 to this model, thus enabling rapid species delimitation on large molecular datasets and allowing the use of relaxed molecular clock models. We validate these methods with genomic sequence data and SNP data, and show they are more efficient than existing methods at achieving parameter convergence during Bayesian MCMC. Lastly, we apply these methods to two datasets (Hemidactylus and Galagidae) and find inconsistencies with the published literature. Our methods are powerful for rapid quantitative testing of species boundaries in large multilocus datasets and are implemented as an open source BEAST 2 package called SPEEDEMON. Introducing SPEEDEMON, a package for BEAST 2 that better defines species boundaries based on molecular data demonstrated on gecko and loris datasets.
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Affiliation(s)
- Jordan Douglas
- School of Computer Science, The University of Auckland, Auckland, New Zealand.
| | - Remco Bouckaert
- School of Computer Science, The University of Auckland, Auckland, New Zealand
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The evolution of primate malaria parasites: A study on the origin and diversification of Plasmodium in lemurs. Mol Phylogenet Evol 2022; 174:107551. [PMID: 35690381 DOI: 10.1016/j.ympev.2022.107551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022]
Abstract
Among the primate malaria parasites, those found in lemurs have been neglected. Here, six Plasmodium lineages were detected in 169 lemurs. Nearly complete mitochondrial genomes (mtDNA, ≈6Kb) and apicoplast loci (≈6Kb) were obtained from these parasites and other Haemosporida species. Plasmodium spp. in lemurs are a diverse clade that shares a common ancestor with other primate parasites from continental Africa. Time-trees for the mtDNA were estimated under different scenarios, and the origin of the lemur clade coincides with the proposed time of their host species' most recent common ancestor (Lemuridae-Indriidae). A time tree with fewer taxa was estimated with mtDNA + Apicoplast loci. Those time estimates overlapped but were younger and had narrower credibility intervals than those from mtDNA alone. Importantly, the mtDNA + Apicoplast estimates that the clade including the most lethal malaria parasite in humans, Plasmodium falciparum, may have originated with Homininae (African apes). Finally, the phylogenetic congruence of the lemurs and their parasites was explored. A statistically significant scenario identified four cospeciation, two duplications, four transfer (host-switches), and zero loss events. Thus, the parasite species sampled in lemurs seem to be radiating with their hosts.
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6
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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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7
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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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Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA. Primates 2021; 62:667-675. [PMID: 33909155 DOI: 10.1007/s10329-021-00912-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations.
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9
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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10
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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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11
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Doyle ED, Prates I, Sampaio I, Koiffmann C, Silva WA, Carnaval AC, Harris EE. Molecular phylogenetic inference of the howler monkey radiation (Primates: Alouatta). Primates 2020; 62:177-188. [PMID: 32876810 DOI: 10.1007/s10329-020-00854-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Howler monkeys (Alouatta), comprising between nine and 14 species and ranging from southern Mexico to northern Argentina, are the most widely distributed platyrrhines. Previous phylogenetic studies of howlers have used chromosomal and morphological characters and a limited number of molecular markers; however, branching patterns conflict between studies or remain unresolved. We performed a new phylogenetic analysis of Alouatta using both concatenated and coalescent-based species tree approaches based on 14 unlinked non-coding intergenic nuclear regions. Our taxon sampling included five of the seven South American species (Alouatta caraya, Alouatta belzebul, Alouatta guariba, Alouatta seniculus, Alouatta sara) and the two recognized species from Mesoamerica (Alouatta pigra, Alouatta palliata). Similarly to previous studies, our phylogenies supported a Mesoamerican clade and a South American clade. For the South American howlers, both methods recovered the Atlantic Forest endemic A. guariba as sister to all remaining South American species, albeit with moderate support. Moreover, we found no support for the previously proposed sister relationship between A. guariba and A. belzebul. For the first time, a clade composed of A. sara and A. caraya was identified. The relationships among the other South American howlers, however, were not fully supported. Our estimates for divergence times within Alouatta are generally older compared to estimates in earlier studies. However, they conform to recent studies proposing a Miocene age for the Isthmus of Panama and for the uplift of the northern Andes. Our results also point to an early genetic isolation of A. guariba in the Atlantic Forest, in agreement with the hypothesis of biotic exchange across South American rain forests in the Miocene. Collectively, these findings contribute to a better understanding of the diversification processes among howler monkey species; however, they also suggest that further comprehension of the evolutionary history of the Alouatta radiation will rely on broadened taxonomic, geographic, and genomic sampling.
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Affiliation(s)
| | - Ivan Prates
- Department of Biology, City College of New York, New York, NY, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal Do Pará, Campus de Bragança, Belém, PA, Brazil
| | - Celia Koiffmann
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Wilson Araujo Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, NY, USA
- The Graduate Center, The City University of New York, New York, NY, USA
| | - Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, The City University of New York, New York, NY, USA.
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12
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Finnie KR, Jones CP, Dupont WD, Salleng KJ, Shuster KA. A Comparison of the Efficacy and Cardiopulmonary Effects of 3 Different Sedation Protocols in Otolemur garnettii. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2020; 59:557-566. [PMID: 32693866 PMCID: PMC7479768 DOI: 10.30802/aalas-jaalas-19-000158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Northern greater galago (Otolemur garnettii) is a prosimian primate most commonly used to study the evolutionary development of vision and somatosensation. This study aimed to investigate the efficacy and cardiopulmonary effects of 3 sedation protocols commonly used in other primate species: 1) alfaxalone (Alf; 8 mg/kg IM) 2) ketamine alone (Ket; 20 mg/kg IM) and 3) ketamine + dexmedetomidine (Ket+Dex; 4 mg/kg + 25 μg/kg IM) with reversal (atipamezole; 250 μg/kg IM). A total of 34 animals were evaluated, including 11 juveniles and 23 adults. Cardiopulmonary parameters such as indirect blood pressure, heart rate, respiratory rate, and SpO₂ were measured, and blood was collected for blood gas analysis and a chemistry panel. To examine the efficacy of each sedation protocol, induction time, immobilization time, and recovery time were recorded. Subjective measures of quality and efficacy included quality of induction, pedal withdrawal reflex, palpebral reflex, muscle tension, rectal temperature, and quality of recovery. All 3 protocols successfully immobilized the animals and all animals recovered from sedation. Heart rates were highest among the Ket group and the lowest for the Ket+Dex group. On average, the Alf group was immobilized for twice as long as either the Ket or Ket+Dex groups. The Ket+Dex group had the fastest average recovery time and subjectively had the best quality of recovery. Based on these results, Ket+Dex is recommended over Alf or Ket alone for brief sedation of healthy galagos.
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Key Words
- be, base excess
- bp, blood pressure
- ck, creatine kinase
- dap, diastolic arterial blood pressure
- hco3, bicarbonate
- hr, heart rate
- map, mean arterial blood pressure
- rr, respiratory rate
- sap, systolic arterial blood pressure
- spo2, oxygen-hemoglobin saturation
- so2, oxygen saturation
- tco2, total blood carbon dioxide
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Affiliation(s)
- Kelsey R Finnie
- Division of Comparative Medicine, and,Corresponding author.
| | | | - William D Dupont
- Department of Biostatistics,Vanderbilt University Medical Center, Nashville, Tennessee
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13
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Godfrey LR, Samonds KE, Baldwin JW, Sutherland MR, Kamilar JM, Allfisher KL. Mid-Cenozoic climate change, extinction, and faunal turnover in Madagascar, and their bearing on the evolution of lemurs. BMC Evol Biol 2020; 20:97. [PMID: 32770933 PMCID: PMC7414565 DOI: 10.1186/s12862-020-01628-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/18/2020] [Indexed: 01/16/2023] Open
Abstract
Background Was there a mid-Cenozoic vertebrate extinction and recovery event in Madagascar and, if so, what are its implications for the evolution of lemurs? The near lack of an early and mid-Cenozoic fossil record on Madagascar has inhibited direct testing of any such hypotheses. We compare the terrestrial vertebrate fauna of Madagascar in the Holocene to that of early Cenozoic continental Africa to shed light on the probability of a major mid-Cenozoic lemur extinction event, followed by an “adaptive radiation” or recovery. We also use multiple analytic approaches to test competing models of lemur diversification and the null hypothesis that no unusual mid-Cenozoic extinction of lemurs occurred. Results Comparisons of the terrestrial vertebrate faunas of the early Cenozoic on continental Africa and Holocene on Madagascar support the inference that Madagascar suffered a major mid-Cenozoic extinction event. Evolutionary modeling offers some corroboration, although the level of support varies by phylogeny and model used. Using the lemur phylogeny and divergence dates generated by Kistler and colleagues, RPANDA and TESS offer moderate support for the occurrence of unusual extinction at or near the Eocene-Oligocene (E-O) boundary (34 Ma). TreePar, operating under the condition of obligate mass extinction, found peak diversification at 31 Ma, and low probability of survival of prior lineages. Extinction at the E-O boundary received greater support than other candidate extinctions or the null hypothesis of no major extinction. Using the lemur phylogeny and divergence dates generated by Herrera & Dàvalos, evidence for large-scale extinction diminishes and its most likely timing shifts to before 40 Ma, which fails to conform to global expectations. Conclusions While support for large-scale mid-Cenozoic lemur extinction on Madagascar based on phylogenetic modeling is inconclusive, the African fossil record does provide indirect support. Furthermore, a major extinction and recovery of lemuriforms during the Eocene-Oligocene transition (EOT) would coincide with other major vertebrate extinctions in North America, Europe, and Africa. It would suggest that Madagascar’s lemurs were impacted by the climate shift from “greenhouse” to “ice-house” conditions that occurred at that time. This could, in turn, help to explain some of the peculiar characteristics of the lemuriform clade.
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Affiliation(s)
- Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.
| | - Karen E Samonds
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Justin W Baldwin
- Department of Public Health, School of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA.,Present Address: Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Michael R Sutherland
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jason M Kamilar
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA
| | - Kristen L Allfisher
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.,Present Address: USDA, APHIS, Riverdale, MD, 20737, USA
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14
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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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15
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Phukuntsi MA, Du Plessis M, Dalton DL, Jansen R, Cuozzo FP, Sauther ML, Kotze A. Population genetic structure of the thick-tailed bushbaby ( Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 31:1-10. [PMID: 31762360 DOI: 10.1080/24701394.2019.1694015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.
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Affiliation(s)
- Metlholo Andries Phukuntsi
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Environment, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Morne Du Plessis
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Biotechnology, University of Western Cape, Cape Town, South Africa
| | - Desiré Lee Dalton
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Raymond Jansen
- Department of Environment, Water and Earth Sciences, Tshwane University of Technology, Pretoria, South Africa
| | | | | | - Antoinette Kotze
- South African National Biodiversity Institute, Pretoria, South Africa.,Department of Genetics, University of the Free State, Bloemfontein, South Africa
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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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Tavares WC, Seuánez HN. Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PLoS One 2017; 12:e0177403. [PMID: 28510580 PMCID: PMC5433710 DOI: 10.1371/journal.pone.0177403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/26/2017] [Indexed: 01/09/2023] Open
Abstract
Several human diseases have been associated with mutations in mitochondrial genes comprising a set of confirmed and reported mutations according to the MITOMAP database. An analysis of complete mitogenomes across 139 primate species showed that most confirmed disease-associated mutations occurred in aligned codon positions and gene regions under strong purifying selection resulting in a strong evolutionary conservation. Only two confirmed variants (7.1%), coding for the same amino acids accounting for severe human diseases, were identified without apparent pathogenicity in non-human primates, like the closely related Bornean orangutan. Conversely, reported disease-associated mutations were not especially concentrated in conserved codon positions, and a large fraction of them occurred in highly variable ones. Additionally, 88 (45.8%) of reported mutations showed similar variants in several non-human primates and some of them have been present in extinct species of the genus Homo. Considering that recurrent mutations leading to persistent variants throughout the evolutionary diversification of primates are less likely to be severely damaging to fitness, we suggest that these 88 mutations are less likely to be pathogenic. Conversely, 69 (35.9%) of reported disease-associated mutations occurred in extremely conserved aligned codon positions which makes them more likely to damage the primate mitochondrial physiology.
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Affiliation(s)
- William Corrêa Tavares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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19
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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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20
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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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21
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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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22
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Herrera JP. Testing the adaptive radiation hypothesis for the lemurs of Madagascar. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161014. [PMID: 28280597 PMCID: PMC5319363 DOI: 10.1098/rsos.161014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 05/12/2023]
Abstract
Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.
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Affiliation(s)
- James P. Herrera
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Author for correspondence: James P. Herrera e-mail:
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23
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Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
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24
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Schneiderová I, Zouhar J, Štefanská L, Bolfíková BČ, Lhota S, Brandl P. Vocal activity of lesser galagos (Galago spp.) at zoos. Zoo Biol 2016; 35:147-56. [PMID: 26741794 DOI: 10.1002/zoo.21261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/16/2015] [Indexed: 11/06/2022]
Abstract
Almost nothing is known about the natural vocal behavior of lesser galagos living in zoos. This is perhaps because they are usually kept in nocturnal exhibits separated from the visitors by a transparent and acoustically insulating glass barrier. The aim of the present study was therefore to fill this gap in knowledge of the vocal behavior of lesser galagos from zoos. This knowledge might be beneficial because the vocalizations of these small primates can be used for species determination. We performed a 10-day-long acoustic monitoring of vocal activity in each of seven various groups of Galago senegalensis and G. moholi living at four zoos. We quantitatively evaluated the occurrence of four loud vocalization types present in both species, including the most species-specific advertisement call. We found that qualitative as well as quantitative differences exist in the vocal behavior of the studied groups. We confirmed that the observed vocalization types can be collected from lesser galagos living at zoos, and the success can be increased by selecting larger and more diverse groups. We found two distinct patterns of diel vocal activity in the most vocally active groups. G. senegalensis groups were most vocally active at the beginning and at the end of their activity period, whereas one G. moholi group showed an opposite pattern. The latter is surprising, as it is generally accepted that lesser galagos emit advertisement calls especially at dawn and dusk, i.e., at the beginning and at the end of their diel activity.
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Affiliation(s)
- Irena Schneiderová
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Zouhar
- Department of Econometrics, Faculty of Informatics and Statistics, University of Economics, Prague, Czech Republic
| | - Lucie Štefanská
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical Agrisciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Stanislav Lhota
- Department of Husbandry and Ethology of Animals, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czech Republic.,Ústí nad Labem Zoo, Ústí nad Labem, Czech Republic
| | - Pavel Brandl
- Prague Zoological Garden, Prague, Czech Republic
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Burrows AM, Hartstone-Rose A, Nash LT. Exudativory in the Asian loris,Nycticebus: Evolutionary divergence in the toothcomb and M3. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:663-72. [DOI: 10.1002/ajpa.22829] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Anne M. Burrows
- Department of Physical Therapy; Duquesne University; Pittsburgh PA 15282
- Department of Anthropology; University of Pittsburgh; Pittsburgh PA 15260
| | - Adam Hartstone-Rose
- Department of Cell Biology and Anatomy; the University of South Carolina School of Medicine; SC 29209 Columbia
| | - Leanne T. Nash
- School of Human Evolution and Social Change; Arizona State University; Tempe AZ 85287-2402
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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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Pozzi L, Nekaris KAI, Perkin A, Bearder SK, Pimley ER, Schulze H, Streicher U, Nadler T, Kitchener A, Zischler H, Zinner D, Roos C. Remarkable ancient divergences amongst neglected lorisiform primates. Zool J Linn Soc 2015; 175:661-674. [PMID: 26900177 PMCID: PMC4744660 DOI: 10.1111/zoj.12286] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 11/29/2022]
Abstract
Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub-Saharan Africa and South/South-East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group.
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Affiliation(s)
- Luca Pozzi
- Behavioral Ecology and Sociobiology Unit German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
| | | | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes UniversityOxfordOX3 0BPUK; Tanzania Forest Conservation GroupPO Box 23410Dar es SalaamTanzania
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University Oxford OX3 0BP UK
| | - Elizabeth R Pimley
- Nocturnal Primate Research Group, Oxford Brookes UniversityOxfordOX3 0BPUK; School of Natural & Social SciencesUniversity of GloucestershireFrancis Close HallSwindon RoadCheltenhamGloucestershireGL50 4AZUK
| | - Helga Schulze
- Department of Neuroanatomy MA 01/43 Ruhr University 44780 Bochum Germany
| | | | - Tilo Nadler
- Endangered Primate Rescue Center, Cuc Phuong National Park Nho Quan District, Ninh Binh Province Vietnam
| | - Andrew Kitchener
- Department of Natural SciencesNational Museums ScotlandChambers StreetEdinburghEH1 1JFUK; Institute of GeographySchool of GeoSciencesUniversity of EdinburghDrummond StreetEdinburghEH8 9XPUK
| | - Hans Zischler
- Institute of Anthropology University of Mainz Anselm-Franz-von-Bentzel-Weg 7 55128 Mainz Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
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Cadamuro VC, Bouakaze C, Croze M, Schiavinato S, Tonasso L, Gérard P, Fausser JL, Gibert M, Dugoujon JM, Braga J, Balaresque P. Determined about sex: sex-testing in 45 primate species using a 2Y/1X sex-typing assay. Forensic Sci Int Genet 2014; 14:96-107. [PMID: 25307201 DOI: 10.1016/j.fsigen.2014.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/04/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022]
Abstract
Sex-testing using molecular genetic technique is routinely used in the fields of forensics, population genetics and conservation biology. However, none of the assay used so far allows a non-ambiguous and successful sex determination for human and non-human primate species. The most widely used method, AMELY/X, and its alternatives suffer from a set of drawbacks in humans and can rarely be used in New World primate species. Here, we designed a new sex-typing assay using a multiplexed PCR amplification of UTX and UTY-homologous loci and combined male-specific SRY locus. This method was successfully tested on 1048 samples, including 82 non-human primates from 45 Anthropoidea and Lemuriformes species and 966 human samples from 24 populations (Africans, Europeans, and South Americans). This sex-typing method is applicable across all primate species tested from Hominoidea to Indriidae, and also on various populations with different background origins; it represents a robust and cheap sex-typing assay to be used both by the anthropologist and primatologist communities.
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Affiliation(s)
- Valérie Choesmel Cadamuro
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Caroline Bouakaze
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; Evolutionary Biology team, Department of Biology II, Ludwig Maximilian University of Munich, LMU BioCenter, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Stéphanie Schiavinato
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Laure Tonasso
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Patrice Gérard
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Jean-Luc Fausser
- Laboratoire AMIS-UMR5288/CNRS, Institut de Médecine Légale, 11 rue Humann, 67085 Strasbourg Cedex, France
| | - Morgane Gibert
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Jean-Michel Dugoujon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - José Braga
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Patricia Balaresque
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2014; 75:165-83. [PMID: 24583291 PMCID: PMC4059600 DOI: 10.1016/j.ympev.2014.02.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 01/23/2023]
Abstract
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
| | - Jason A Hodgson
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Andrew S Burrell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States.
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, OR, United States.
| | - Ryan L Raaum
- New York Consortium in Evolutionary Primatology, United States; Department of Anthropology, Lehman College & The Graduate Center, City University of New York, Bronx, NY, United States.
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States.
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