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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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2
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Stoessel A, David R, Bornitz M, Ossmann S, Neudert M. Auditory thresholds compatible with optimal speech reception likely evolved before the human-chimpanzee split. Sci Rep 2023; 13:20732. [PMID: 38007561 PMCID: PMC10676368 DOI: 10.1038/s41598-023-47778-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
The anatomy of the auditory region of fossil hominins may shed light on the emergence of human spoken language. Humans differ from other great apes in several features of the external, middle and inner ear (e.g., short external ear canal, small tympanic membrane, large oval window). However, the functional implications of these differences remain poorly understood as comparative audiometric data from great apes are scarce and conflicting. Here, we measure the sound transfer function of the external and middle ears of humans, chimpanzees and bonobos, using laser-Doppler vibrometry and finite element analysis. This sound transfer function affects auditory thresholds, which relate to speech reception thresholds in humans. Unexpectedly we find that external and middle ears of chimpanzees and bonobos transfer sound better than human ones in the frequency range of spoken language. Our results suggest that auditory thresholds of the last common ancestor of Homo and Pan were already compatible with speech reception as observed in humans. Therefore, it seems unlikely that the morphological evolution observed in the bony auditory region of fossil hominins was driven by the emergence of spoken language. Instead, the peculiar human configuration may be a by-product of morpho-functional constraints linked to brain expansion.
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Affiliation(s)
- Alexander Stoessel
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Erbertstr. 1, 07743, Jena, Germany.
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Romain David
- Centre for Human Evolution Research, The Natural History Museum, Cromwell Rd, South Kensington, London, SW7 5BD, UK.
| | - Matthias Bornitz
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Steffen Ossmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Marcus Neudert
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
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3
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Carneiro J, Sampaio I, Silva-Júnior JDSE, Martins-Junior A, Farias I, Hrbek T, Boubli J, Schneider H. Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini). Genes (Basel) 2023; 14:1309. [PMID: 37510215 PMCID: PMC10379672 DOI: 10.3390/genes14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 07/30/2023] Open
Abstract
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes.
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Affiliation(s)
- Jeferson Carneiro
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | | | - Antonio Martins-Junior
- Federal Institute of Education, Science and Technology of Pará, Campus Tucuruí, Tucuruí 68455-210, Pará, Brazil
| | - Izeni Farias
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Horacio Schneider
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
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4
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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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5
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Guilfoyle KJ, McIntosh AM, Hatch KA. Seasonal differences in hair growth rates of captive aye-aye, red ruffed, and black-and-white ruffed lemurs. Zoo Biol 2023; 42:112-118. [PMID: 35733330 DOI: 10.1002/zoo.21715] [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: 05/05/2021] [Revised: 04/26/2022] [Accepted: 06/07/2022] [Indexed: 11/11/2022]
Abstract
Hair can be an important source of biological information, providing a record of such things as pollutant exposure, hormonal levels, and stable isotope ratios. Hair as a biological sample is easily accessible, easily stored, and resists degradation. Analysis of hair is particularly useful when studying rare and endangered species, such as lemurs, since it can be sampled noninvasively. However, to better interpret the results of stable isotope or other analyses, it is important to understand hair growth rates. We measured hair growth rates in captive aye-ayes (Daubentonia madagascariensis), red ruffed lemurs (Varecia rubra), and black-and-white ruffed lemurs (Varecia variegata), both in winter (December 23, 2013, to January 13, 2014) and summer (July 10-31, 2013) at the Duke Lemur Center. Hair growth per week in all three species of lemurs differed significantly between the boreal summer and boreal winter. The aye-aye, black-and-white ruffed lemur, red ruffed lemur had a mean weekly hair growth of 0.195, 0.209, and 0.232 cm, respectively, in the summer. While the aye-aye, black-and-white ruffed lemur, and red ruffed lemur had a mean weekly hair growth of 0.239, 0.464, and 0.479 cm, respectively, in winter. We found no effect of age on hair growth rates, neither in the boreal summer, nor in the boreal winter for black-and-white ruffed lemurs and red ruffed lemurs. A pregnant black-and-white ruffed female displayed negligible hair growth during the northern winter, suggesting that pregnancy may affect the partitioning of resources away from such things as hair growth.
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Affiliation(s)
- Kevin J Guilfoyle
- Department of Biological and Environmental Sciences, Long Island University, Brookville, New York, USA
| | - Apryl M McIntosh
- Department of Biological and Environmental Sciences, Long Island University, Brookville, New York, USA
| | - Kent A Hatch
- Department of Biological and Environmental Sciences, Long Island University, Brookville, New York, USA
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6
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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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7
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Phylogenetics and an updated taxonomic status of the Tamarins (Callitrichinae, Cebidae). Mol Phylogenet Evol 2022; 173:107504. [DOI: 10.1016/j.ympev.2022.107504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022]
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8
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Donohue ME, Rowe AK, Kowalewski E, Hert ZL, Karrick CE, Randriamanandaza LJ, Zakamanana F, Nomenjanahary S, Andriamalala RY, Everson KM, Law AD, Moe L, Wright PC, Weisrock DW. Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME COMMUNICATIONS 2022; 2:33. [PMID: 37938265 PMCID: PMC9723590 DOI: 10.1038/s43705-022-00115-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 04/27/2023]
Abstract
Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, NY, USA
| | - Eric Kowalewski
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Zoe L Hert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | | | - Stela Nomenjanahary
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | - Rostant Y Andriamalala
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | | | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Luke Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Madagascar
- Department of Anthropology, Stony Brook University, Stony Brook, New York, NY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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9
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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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Guevara EE, Greene LK, Blanco MB, Farmer C, Ranaivonasy J, Ratsirarson J, Mahefarisoa KL, Rajaonarivelo T, Rakotondrainibe HH, Junge RE, Williams CV, Rambeloson E, Rasoanaivo HA, Rahalinarivo V, Andrianandrianina LH, Clayton JB, Rothman RS, Lawler RR, Bradley BJ, Yoder AD. Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.736741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
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11
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Fulwood EL, Shan S, Winchester JM, Kirveslahti H, Ravier R, Kovalsky S, Daubechies I, Boyer DM. Insights from macroevolutionary modelling and ancestral state reconstruction into the radiation and historical dietary ecology of Lemuriformes (Primates, Mammalia). BMC Ecol Evol 2021; 21:60. [PMID: 33882818 PMCID: PMC8061064 DOI: 10.1186/s12862-021-01793-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/11/2021] [Indexed: 01/16/2023] Open
Abstract
Background Lemurs once rivalled the diversity of rest of the primate order despite thier confinement to the island of Madagascar. We test the adaptive radiation model of Malagasy lemur diversity using a novel combination of phylogenetic comparative methods and geometric methods for quantifying tooth shape. Results We apply macroevolutionary model fitting approaches and disparity through time analysis to dental topography metrics associated with dietary adaptation, an aspect of mammalian ecology which appears to be closely related to diversification in many clades. Metrics were also reconstructed at internal nodes of the lemur tree and these reconstructions were combined to generate dietary classification probabilities at internal nodes using discriminant function analysis. We used these reconstructions to calculate rates of transition toward folivory per million-year intervals. Finally, lower second molar shape was reconstructed at internal nodes by modelling the change in shape of 3D meshes using squared change parsimony along the branches of the lemur tree. Our analyses of dental topography metrics do not recover an early burst in rates of change or a pattern of early partitioning of subclade disparity. However, rates of change in adaptations for folivory were highest during the Oligocene, an interval of possible forest expansion on the island. Conclusions There was no clear phylogenetic signal of bursts of morphological evolution early in lemur history. Reconstruction of the molar morphologies corresponding to the ancestral nodes of the lemur tree suggest that this may have been driven by a shift toward defended plant resources, however. This suggests a response to the ecological opportunity offered by expanding forests, but not necessarily a classic adaptive radiation initiated by dispersal to Madagascar. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01793-x.
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Affiliation(s)
- Ethan L Fulwood
- Department of Biomedical Sciences, Kentucky College of Osteopathic Medicine, Pikeville, KY, 41501, USA. .,Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA.
| | - Shan Shan
- Department of Mathematics, Duke University, Durham, NC, 27708, USA
| | - Julia M Winchester
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Henry Kirveslahti
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | - Robert Ravier
- Department of Mathematics, Duke University, Durham, NC, 27708, USA.,Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Shahar Kovalsky
- Department of Mathematics, Duke University, Durham, NC, 27708, USA
| | - Ingrid Daubechies
- Department of Mathematics, Duke University, Durham, NC, 27708, USA.,Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Doug M Boyer
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
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12
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Shearn R, Wright AE, Mousset S, Régis C, Penel S, Lemaitre JF, Douay G, Crouau-Roy B, Lecompte E, Marais GA. Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates. eLife 2020; 9:63650. [PMID: 33205751 PMCID: PMC7717902 DOI: 10.7554/elife.63650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Sex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex-chromosome biology both from a functional and evolutionary perspective. The evolution of the pseudoautosomal boundary (PAB) is well documented in haplorrhines (apes and monkeys) but not in strepsirrhines (lemurs and lorises). Here, we studied the PAB of seven species representing the main strepsirrhine lineages by sequencing a male and a female genome in each species and using sex differences in coverage to identify the PAB. We found that during primate evolution, the PAB has remained unchanged in strepsirrhines whereas several recombination suppression events moved the PAB and shortened the pseudoautosomal region in haplorrhines. Strepsirrhines are well known to have much lower sexual dimorphism than haplorrhines. We suggest that mutations with antagonistic effects between males and females have driven recombination suppression and PAB evolution in haplorrhines.
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Affiliation(s)
- Rylan Shearn
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sylvain Mousset
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France.,Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Corinne Régis
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | - Simon Penel
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | | | | | - Brigitte Crouau-Roy
- Laboratoire Evolution et Diversité Biologique, CNRS / Univ. Toulouse, Toulouse, France
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité Biologique, CNRS / Univ. Toulouse, Toulouse, France
| | - Gabriel Ab Marais
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France.,LEAF-Linking Landscape, Environment, Agriculture and Food Dept, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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13
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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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De Petrillo F, Rosati AG. Logical inferences from visual and auditory information in ruffed lemurs and sifakas. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Sumampow TCP, Shekelle M, Beier P, Walker FM, Hepp CM. Identifying genetic relationships among tarsier populations in the islands of Bunaken National Park and mainland Sulawesi. PLoS One 2020; 15:e0230014. [PMID: 32214331 PMCID: PMC7098592 DOI: 10.1371/journal.pone.0230014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 11/22/2022] Open
Abstract
Eastern tarsiers (Tarsius tarsier complex) are small nocturnal primates endemic to Sulawesi Island and small adjacent islands of Indonesia. In 2004, the hybrid biogeography hypothesis predicted this species complex might contain 16 or more taxa, each corresponding to a region of endemism, based on: 1) geological evidence of the development of the archipelago, 2) biological evidence in the form of concordant distributions of monkeys and toads, and 3) the distribution of tarsier acoustic groups. Since then, 11 tarsier species have been recognized, potentially leaving more to be described. Efforts to identify these cryptic species are urgently needed so that habitat conversion, pet trade, and cultural activities will not render some species extinct before they are recognized. We gathered data to test the hypothesis of cryptic tarsier species on three volcanic islands in Bunaken National Park, North Sulawesi, namely Bunaken, Manadotua, and Mantehage, during May-August 2018. We sequenced individuals at 5 nuclear genes (ABCA1, ADORA3, AXIN1, RAG, and TTR) and made comparisons to existing genotypes at 14 mainland sites. Bayesian phylogenetic analyses revealed that island populations are genetically identical in all 5 genes, and formed a clade separated from the mainland ones. The eastern tarsiers first diverged from the western tarsiers approximately 2.5 MYA. The three island populations diverged from mainland tarsiers approximately 2,000-150,000 YA, due to either human activities or natural rafting. This study provides information for tarsier conservation, advances the understanding of biogeography of Sulawesi, and contributes to Indonesian awareness of biodiversity. Further quantitative genetics research on tarsiers, especially the island populations, will offer significant insights to establish more efficient and strategic tarsier conservation actions.
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Affiliation(s)
| | - Myron Shekelle
- Western Washington University, Bellingham, WA, United States of America
| | - Paul Beier
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Faith M. Walker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
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16
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Saraf MP, Balaram P, Pifferi F, Kennedy H, Kaas JH. The sensory thalamus and visual midbrain in mouse lemurs. J Comp Neurol 2019; 527:2599-2611. [PMID: 30927368 DOI: 10.1002/cne.24693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/24/2022]
Abstract
Mouse lemurs are the smallest of extant primates and are thought to resemble early primates in many ways. We provide histological descriptions of the major sensory nuclei of the dorsal thalamus and the superior colliculus (SC) of mouse lemurs (Microcebus murinus). The dorsal lateral geniculate nucleus has the six layers typical of strepsirrhine primates, with matching pairs of magnocellular, parvocellular, and koniocellular layers, one of each pair for each eye. Unlike most primates, magnocellular and parvocellular layers exhibit only small differences in cell size. All layers express vesicular glutamate transporter 2 (VGLUT2), reflecting terminations of retinal inputs, and the expression of VGLUT2 is much less dense in the koniocellular layers. Parvalbumin is densely expressed in all layers, while SMI-32 is densely expressed only in the magnocellular layers. The adjoining pulvinar complex has a posterior nucleus with strong VGLUT2 expression, reflecting terminations from the SC. The SC is laminated with dense expression of VGLUT2 in the upper superficial gray layer, reflecting terminations from the retina. The ventral (MGNv), medial, and dorsal divisions of the medial geniculate complex are only moderately differentiated, although patches of dense VGLUT2 expression are found along the outer border of MGNv. The ventroposterior nucleus has darkly stained cells in Nissl stained sections, and narrow septa separating patchy regions of dense VGLUT2 expression that likely represent different body parts. Overall, these structures resemble those in other strepsirrhine primates, although they are smaller, with the sensory nuclei appearing to occupy proportionately more of the dorsal thalamus than in larger primates.
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Affiliation(s)
- Mansi P Saraf
- Department of Psychology, Vanderbilt University, Nashville, Tennessee
| | - Pooja Balaram
- Department of Psychology, Vanderbilt University, Nashville, Tennessee
| | - Fabien Pifferi
- MECADEV UMR 7179, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Brunoy, France
| | - Henry Kennedy
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, Bron, France.,Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Chinese Academy of Science (CAS), Shanghai, China
| | - Jon H Kaas
- Department of Psychology, Vanderbilt University, Nashville, Tennessee
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17
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Greene LK, Bornbusch SL, McKenney EA, Harris RL, Gorvetzian SR, Yoder AD, Drea CM. The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs. Am J Primatol 2019; 81:e22974. [PMID: 30932230 DOI: 10.1002/ajp.22974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022]
Abstract
Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host-microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage-specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent-gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host-microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis-driven research.
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Affiliation(s)
- Lydia K Greene
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Sally L Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Rachel L Harris
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Sarah R Gorvetzian
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, North Carolina
| | - Christine M Drea
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Department of Biology, Duke University, Durham, North Carolina
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18
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Saraf MP, Balaram P, Pifferi F, Gămănuţ R, Kennedy H, Kaas JH. Architectonic features and relative locations of primary sensory and related areas of neocortex in mouse lemurs. J Comp Neurol 2018; 527:625-639. [PMID: 29484648 DOI: 10.1002/cne.24419] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/27/2022]
Abstract
Mouse lemurs are the smallest of the living primates, and are members of the understudied radiation of strepsirrhine lemurs of Madagascar. They are thought to closely resemble the ancestral primates that gave rise to present day primates. Here we have used multiple histological and immunochemical methods to identify and characterize sensory areas of neocortex in four brains of adult lemurs obtained from a licensed breeding colony. We describe the laminar features for the primary visual area (V1), the secondary visual area (V2), the middle temporal visual area (MT) and area prostriata, somatosensory areas S1(3b), 3a, and area 1, the primary motor cortex (M1), and the primary auditory cortex (A1). V1 has "blobs" with "nonblob" surrounds, providing further evidence that this type of modular organization might have evolved early in the primate lineage to be retained in all extant primates. The laminar organization of V1 further supports the view that sublayers of layer 3 of primates have been commonly misidentified as sublayers of layer 4. S1 (area 3b) is proportionately wider than the elongated area observed in anthropoid primates, and has disruptions that may distinguish representations of the hand, face, teeth, and tongue. Primary auditory cortex is located in the upper temporal cortex and may include a rostral area, R, in addition to A1. The resulting architectonic maps of cortical areas in mouse lemurs can usefully guide future studies of cortical connectivity and function.
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Affiliation(s)
- Mansi P Saraf
- Department of Psychology, Vanderbilt University, Nashville, TN, 37240
| | - Pooja Balaram
- Department of Psychology, Vanderbilt University, Nashville, TN, 37240.,MECADEV UMR 7179, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Brunoy, 91800, France
| | - Fabien Pifferi
- Université de Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, Bron, 69500, France
| | - Răzvan Gămănuţ
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Science (CAS) Key Laboratory of Primate Neurobiology, CAS, Shanghai, 200031, China
| | - Henry Kennedy
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Science (CAS) Key Laboratory of Primate Neurobiology, CAS, Shanghai, 200031, China
| | - Jon H Kaas
- Department of Psychology, Vanderbilt University, Nashville, TN, 37240
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19
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Sgarlata GM, Salmona J, Aleixo-Pais I, Rakotonanahary A, Sousa AP, Kun-Rodrigues C, Ralantoharijaona T, Jan F, Zaranaina R, Rasolondraibe E, Zaonarivelo JR, Andriaholinirina NV, Chikhi L. Genetic Differentiation and Demographic History of the Northern Rufous Mouse Lemur (Microcebus tavaratra) Across a Fragmented Landscape in Northern Madagascar. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0015-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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21
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Bolt LM, Tennenhouse E. Contact calling behaviour in the male ring-tailed lemur ( Lemur catta). Ethology 2017. [DOI: 10.1111/eth.12637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Laura M. Bolt
- Department of Anthropology; University of Toronto at Mississauga; Mississauga ON Canada
- Department of Anthropology; University of Toronto; Toronto ON Canada
| | - Erica Tennenhouse
- Department of Anthropology; University of Toronto; Toronto ON Canada
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22
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Fabre AC, Marigó J, Granatosky MC, Schmitt D. Functional associations between support use and forelimb shape in strepsirrhines and their relevance to inferring locomotor behavior in early primates. J Hum Evol 2017. [PMID: 28622924 DOI: 10.1016/j.jhevol.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The evolution of primates is intimately linked to their initial invasion of an arboreal environment. However, moving and foraging in this milieu creates significant mechanical challenges related to the presence of substrates differing in their size and orientation. It is widely assumed that primates are behaviorally and anatomically adapted to movement on specific substrates, but few explicit tests of this relationship in an evolutionary context have been conducted. Without direct tests of form-function relationships in living primates it is impossible to reliably infer behavior in fossil taxa. In this study, we test a hypothesis of co-variation between forelimb morphology and the type of substrates used by strepsirrhines. If associations between anatomy and substrate use exist, these can then be applied to better understand limb anatomy of extinct primates. The co-variation between each forelimb long bone and the type of substrate used was studied in a phylogenetic context. Our results show that despite the presence of significant phylogenetic signal for each long bone of the forelimb, clear support use associations are present. A strong co-variation was found between the type of substrate used and the shape of the radius, with and without taking phylogeny into account, whereas co-variation was significant for the ulna only when taking phylogeny into account. Species that use a thin branch milieu show radii that are gracile and straight and have a distal articular shape that allows for a wide range of movements. In contrast, extant species that commonly use large supports show a relatively robust and curved radius with an increased surface area available for forearm and hand muscles in pronated posture. These results, especially for the radius, support the idea that strepsirrhine primates exhibit specific skeletal adaptations associated with the supports that they habitually move on. With these robust associations in hand it will be possible to explore the same variables in extinct early primates and primate relatives and thus improve the reliability of inferences concerning substrate use in early primates.
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Affiliation(s)
- Anne-Claire Fabre
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA; UMR 7179, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Mécadev, 57 rue Cuvier, CP 55, 75231, Paris Cedex 5, France.
| | - Judit Marigó
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA; UMR 7207 CR2P - C.N.R.S., M.N.H.N., U.P.M.C.-Paris 6, Département Histoire de la Terre, Muséum National d'Histoire Naturelle, 75005, Paris, France; Institut Català de Paleontologia Miquel Crusafont (ICP), Universitat Autònoma de Barcelona, Edifici Z (ICTA-ICP), Carrer de les Columnes s/n, Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Michael C Granatosky
- Department of Organismal Biology and Anatomy, University of Chicago, 60637, Chicago, IL, USA
| | - Daniel Schmitt
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
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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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Grogan KE, McGinnis GJ, Sauther ML, Cuozzo FP, Drea CM. Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications. BMC Genomics 2016; 17:204. [PMID: 26957424 PMCID: PMC4782575 DOI: 10.1186/s12864-016-2503-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/18/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes. RESULTS In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1-7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies. CONCLUSIONS In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species.
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Affiliation(s)
- Kathleen E Grogan
- University Program in Ecology, Duke University, Durham, NC, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.
- Emory University, Room 2006 O. Wayne Rollins Research Center, 1510 Clifton Rd NE, Atlanta, GA, 30322, USA.
| | | | - Michelle L Sauther
- Department of Anthropology, University of Colorado-Boulder, Boulder, CO, USA
| | - Frank P Cuozzo
- Department of Anthropology, University of North Dakota, Grand Forks, ND, USA
| | - Christine M Drea
- University Program in Ecology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, USA
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25
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Byrne H, Rylands AB, Carneiro JC, Alfaro JWL, Bertuol F, da Silva MNF, Messias M, Groves CP, Mittermeier RA, Farias I, Hrbek T, Schneider H, Sampaio I, Boubli JP. Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence. Front Zool 2016; 13:10. [PMID: 26937245 PMCID: PMC4774130 DOI: 10.1186/s12983-016-0142-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background Titi monkeys, Callicebus, comprise the most species-rich primate genus—34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus. Results Our results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups—the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9–8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus. Conclusions Considering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups). Electronic supplementary material The online version of this article (doi:10.1186/s12983-016-0142-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hazel Byrne
- School of Environment and Life Sciences, University of Salford, Room 315, Peel Building, Salford, UK
| | | | - Jeferson C Carneiro
- Universidade Federal do Pará, Campus Universitário de Bragança, Bragança, Pará Brazil
| | - Jessica W Lynch Alfaro
- Department of Anthropology, Institute for Society and Genetics, University of California, Los Angeles, CA USA
| | - Fabricio Bertuol
- Evolution and Animal Genetics Laboratory, Universidade Federal do Amazonas, Manaus, Amazonas Brazil
| | - Maria N F da Silva
- Coleções Zoológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas Brazil
| | | | - Colin P Groves
- School of Archaeology & Anthropology, Australian National University, Canberra, Australia
| | | | - Izeni Farias
- Evolution and Animal Genetics Laboratory, Universidade Federal do Amazonas, Manaus, Amazonas Brazil
| | - Tomas Hrbek
- Evolution and Animal Genetics Laboratory, Universidade Federal do Amazonas, Manaus, Amazonas Brazil
| | - Horacio Schneider
- Universidade Federal do Pará, Campus Universitário de Bragança, Bragança, Pará Brazil
| | - Iracilda Sampaio
- Universidade Federal do Pará, Campus Universitário de Bragança, Bragança, Pará Brazil
| | - Jean P Boubli
- School of Environment and Life Sciences, University of Salford, Room 315, Peel Building, Salford, UK ; Coleções Zoológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas Brazil
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26
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Lei R, McLain AT, Frasier CL, Taylor JM, Bailey CA, Engberg SE, Ginter AL, Nash SD, Randriamampionona R, Groves CP, Mittermeier RA, Louis EE. A New Species in the GenusCheirogaleus(Cheirogaleidae). ACTA ACUST UNITED AC 2015. [DOI: 10.1896/052.029.0103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Driller C, Merker S, Perwitasari-Farajallah D, Sinaga W, Anggraeni N, Zischler H. Stop and Go - Waves of Tarsier Dispersal Mirror the Genesis of Sulawesi Island. PLoS One 2015; 10:e0141212. [PMID: 26559527 PMCID: PMC4641617 DOI: 10.1371/journal.pone.0141212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
The Indonesian island of Sulawesi harbors a highly endemic and diverse fauna sparking fascination since long before Wallace’s contemplation of biogeographical patterns in the region. Allopatric diversification driven by geological or climatic processes has been identified as the main mechanism shaping present faunal distribution on the island. There is both consensus and conflict among range patterns of terrestrial species pointing to the different effects of vicariant events on once co-distributed taxa. Tarsiers, small nocturnal primates with possible evidence of an Eocene fossil record on the Asian mainland, are at present exclusively found in insular Southeast Asia. Sulawesi is hotspot of tarsier diversity, whereby island colonization and subsequent radiation of this old endemic primate lineage remained largely enigmatic. To resolve the phylogeographic history of Sulawesi tarsiers we analyzed an island-wide sample for a set of five approved autosomal phylogenetic markers (ABCA1, ADORA3, AXIN1, RAG1, and TTR) and the paternally inherited SRY gene. We constructed ML and Bayesian phylogenetic trees and estimated divergence times between tarsier populations. We found that their arrival at the Proto-Sulawesi archipelago coincided with initial Miocene tectonic uplift and hypothesize that tarsiers dispersed over the region in distinct waves. Intra-island diversification was spurred by land emergence and a rapid succession of glacial cycles during the Plio-Pleistocene. Some tarsier range boundaries concur with spatial limits in other taxa backing the notion of centers of faunal endemism on Sulawesi. This congruence, however, has partially been superimposed by taxon-specific dispersal patterns.
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Affiliation(s)
- Christine Driller
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
- Department of Biology, Bogor Agricultural University, Bogor, Indonesia
| | - Walberto Sinaga
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
| | - Novita Anggraeni
- School of Graduate Studies, Bogor Agricultural University, Bogor, Indonesia
| | - Hans Zischler
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
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Valenta K, Edwards M, Rafaliarison RR, Johnson SE, Holmes SM, Brown KA, Dominy NJ, Lehman SM, Parra EJ, Melin AD. Visual ecology of true lemurs suggests a cathemeral origin for the primate cone opsin polymorphism. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12575] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kim Valenta
- Department of Anthropology & Archaeology University of Toronto 19 Russell St Toronto ON Canada
| | - Melissa Edwards
- Department of Anthropology University of Toronto at Mississauga 3359 Mississauga Rd. North Mississauga QC Canada
| | | | - Steig E. Johnson
- Department of Anthropology & Archaeology University of Calgary 2500 University Dr. NW. Calgary QC Canada
| | - Sheila M. Holmes
- Department of Anthropology & Archaeology University of Calgary 2500 University Dr. NW. Calgary QC Canada
| | - Kevin A. Brown
- Dalla Lana School of Public Health University of Toronto 155 College St. Toronto QC Canada
| | | | - Shawn M. Lehman
- Department of Anthropology & Archaeology University of Toronto 19 Russell St Toronto ON Canada
| | - Esteban J. Parra
- Department of Anthropology University of Toronto at Mississauga 3359 Mississauga Rd. North Mississauga QC Canada
| | - Amanda D. Melin
- Department of Anthropology Washington University One Brookings Dr. St. Louis MO USA
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Kappeler PM, Fichtel C. Eco-evo-devo of the lemur syndrome: did adaptive behavioral plasticity get canalized in a large primate radiation? Front Zool 2015; 12 Suppl 1:S15. [PMID: 26816515 PMCID: PMC4722368 DOI: 10.1186/1742-9994-12-s1-s15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Comprehensive explanations of behavioral adaptations rarely invoke all levels famously admonished by Niko Tinbergen. The role of developmental processes and plasticity, in particular, has often been neglected. In this paper, we combine ecological, physiological and developmental perspectives in developing a hypothesis to account for the evolution of 'the lemur syndrome', a combination of reduced sexual dimorphism, even adult sex ratios, female dominance and mild genital masculinization characterizing group-living species in two families of Malagasy primates. RESULTS We review the different components of the lemur syndrome and compare it with similar adaptations reported for other mammals. We find support for the assertion that the lemur syndrome represents a unique set of integrated behavioral, demographic and morphological traits. We combine existing hypotheses about underlying adaptive function and proximate causation by adding a potential developmental mechanism linking maternal stress and filial masculinization, and outline an evolutionary scenario for its canalization. CONCLUSIONS We propose a new hypothesis linking ecological, physiological, developmental and evolutionary processes to adumbrate a comprehensive explanation for the evolution of the lemur syndrome, whose assumptions and predictions can guide diverse future research on lemurs. This hypothesis should also encourage students of other behavioral phenomena to consider the potential role of developmental plasticity in evolutionary innovation.
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Affiliation(s)
- Peter M Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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31
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Petty JMA, Drea CM. Female rule in lemurs is ancestral and hormonally mediated. Sci Rep 2015; 5:9631. [PMID: 25950904 PMCID: PMC4423346 DOI: 10.1038/srep09631] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/20/2015] [Indexed: 11/26/2022] Open
Abstract
Female social dominance (FSD) over males is unusual in mammals, yet characterizes most Malagasy lemurs, which represent almost 30% of all primates. Despite its prevalence in this suborder, both the evolutionary trajectory and proximate mechanism of FSD remain unclear. Potentially associated with FSD is a suite of behavioural, physiological and morphological traits in females that implicates (as a putative mechanism) 'masculinization' via androgen exposure; however, relative to conspecific males, female lemurs curiously show little evidence of raised androgen concentrations. By observing mixed-sex pairs of related Eulemur species, we identified two key study groups--one comprised of species expressing FSD and increased female scent marking, the other comprised of species (from a recently evolved clade) showing equal status between the sexes and the more traditional pattern of sexually dimorphic behaviour. Comparing females from these two groups, we show that FSD is associated with more masculine androgen profiles. Based on the widespread prevalence of male-like features in female lemurs and a current phylogeny, we suggest that relaxation of hormonally mediated FSD emerged only recently and that female masculinization may be the ancestral lemur condition, an idea that could revolutionize our understanding of the ancient socioecology and evolution of primate social systems.
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Affiliation(s)
- Joseph M. A. Petty
- University Program in Ecology, Duke University, Durham, NC 27708 USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708 USA
| | - Christine M. Drea
- University Program in Ecology, Duke University, Durham, NC 27708 USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708 USA
- Department of Biology, Duke University, Durham, NC 27708 USA
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32
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Eppley TM, Ganzhorn JU, Donati G. Cathemerality in a small, folivorous primate: proximate control of diel activity in Hapalemur meridionalis. Behav Ecol Sociobiol 2015. [DOI: 10.1007/s00265-015-1911-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Blair C, Noonan BP, Brown JL, Raselimanana AP, Vences M, Yoder AD. Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae). J Evol Biol 2015; 28:481-92. [PMID: 25611210 DOI: 10.1111/jeb.12586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/06/2015] [Indexed: 12/20/2022]
Abstract
Although numerous studies have attempted to find single unifying mechanisms for generating Madagascar's unique flora and fauna, little consensus has been reached regarding the relative importance of climatic, geologic and ecological processes as catalysts of diversification of the region's unique biota. Rather, recent work has shown that both biological and physical drivers of diversification are best analysed in a case-by-case setting with attention focused on the ecological and life-history requirements of the specific phylogenetic lineage under investigation. Here, we utilize a comprehensive analytical approach to examine evolutionary drivers and elucidate the biogeographic history of Malagasy plated lizards (Zonosaurinae). Data from three genes are combined with fossil information to construct time-calibrated species trees for zonosaurines and their African relatives, which are used to test alternative diversification hypotheses. Methods are utilized for explicitly incorporating phylogenetic uncertainty into downstream analyses. Species distribution models are created for 14 of 19 currently recognized species, which are then used to estimate spatial patterns of species richness and endemicity. Spatially explicit analyses are employed to correlate patterns of diversity with both topographic heterogeneity and climatic stability through geologic time. We then use inferred geographic ranges to estimate the biogeographic history of zonosaurines within each of Madagascar's major biomes. Results suggest constant Neogene and Quaternary speciation with divergence from the African most recent common ancestor ~30 million years ago when oceanic currents and African rivers facilitated dispersal. Spatial patterns of diversity appear concentrated along coastal regions of northern and southern Madagascar. We find no relationship between either topographic heterogeneity or climatic stability and patterns of diversity. Ancestral state reconstructions suggest that western dry forests were important centres of origin with recent invasion into spiny and rain forest. These data highlight the power of combining multilocus phylogenetic and spatially explicit analyses for testing alternative diversification hypotheses within Madagascar's unique biota and more generally, particularly as applied to phylogenetically and biologically constrained systems.
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Affiliation(s)
- C Blair
- Department of Biology, Duke University Durham, Durham, NC, USA
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34
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Eppley TM, Hall K, Donati G, Ganzhorn J. An unusual case of affiliative association of a female Lemur catta in a Hapalemur meridionalis social group. BEHAVIOUR 2015. [DOI: 10.1163/1568539x-00003267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Polyspecific associations are well documented, but have rarely been observed in strepsirrhines. In this study we present a unique affiliative association between a female ring-tailed lemur (Lemur catta) and a group of southern bamboo lemurs (Hapalemur meridionalis) in south-east Madagascar. Our main research focused on H. meridionalis; however, due to the presence of the L. catta we treated her as a group member, including her in the focal sampling of Hapalemur social behaviour. We also recorded ad libitum data on all food species/items and any unique events or occurrences. Among observations, both species appeared to have a mutual understanding of vocalisations, behavioural synchronisation, dietary overlap, and possible service exchange, e.g., grooming. We also observed the L. catta occasionally attending to the bamboo lemur infant. This included grooming, baby-sitting, and even transporting the infant. The behavioural flexibility exhibited by both species has allowed the successful integration of the female ring-tailed lemur.
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Affiliation(s)
- Timothy M. Eppley
- aBiozentrum Grindel, Department of Animal Ecology and Conservation, University of Hamburg, Hamburg, Germany
- bNocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Katie Hall
- cMichale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- dNeuroscience Institute & Language Research Center, Georgia State University, Atlanta, GA, USA
| | - Giuseppe Donati
- bNocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Jörg U. Ganzhorn
- aBiozentrum Grindel, Department of Animal Ecology and Conservation, University of Hamburg, Hamburg, Germany
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35
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Hominids adapted to metabolize ethanol long before human-directed fermentation. Proc Natl Acad Sci U S A 2014; 112:458-63. [PMID: 25453080 DOI: 10.1073/pnas.1404167111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol.
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36
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Lei R, Frasier CL, McLain AT, Taylor JM, Bailey CA, Engberg SE, Ginter AL, Randriamampionona R, Groves CP, Mittermeier RA, Jr EEL. Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data. ACTA ACUST UNITED AC 2014. [DOI: 10.1896/052.028.0110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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delBarco-Trillo J, Drea CM. Socioecological and phylogenetic patterns in the chemical signals of strepsirrhine primates. Anim Behav 2014. [DOI: 10.1016/j.anbehav.2014.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ. Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life? Syst Biol 2014; 64:169-86. [DOI: 10.1093/sysbio/syu077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David J. Pattinson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Richard S. Thompson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aleks K. Piotrowski
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Robert J. Asher
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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39
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Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J, Yang Z. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol 2014; 6:213-27. [PMID: 24398377 PMCID: PMC3914689 DOI: 10.1093/gbe/evu006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available.
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40
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Katzourakis A, Aiewsakun P, Jia H, Wolfe ND, LeBreton M, Yoder AD, Switzer WM. Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Retrovirology 2014; 11:61. [PMID: 25091111 PMCID: PMC4261875 DOI: 10.1186/1742-4690-11-61] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/02/2014] [Indexed: 02/06/2023] Open
Abstract
Background Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data. Results Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history. Conclusion Our discovery of ChrEFV has expanded the FV host range to cover the whole eutherian clade, and our evolutionary analyses suggest a stable mammalian FV-host co-speciation pattern which extends as deep as the exafroplacentalian basal diversification. Nonetheless, two possible cases of host switching were observed. One was among New World monkey FVs, and the other involves PSFVaye and a bat FV which may involve cross-species transmission at the level of mammalian orders. Our results highlight the value of integrating multiple sources of information to elucidate the evolutionary history of viruses, including continental and geographical histories, ancestral host locations, in addition to the natural history of host and virus. Electronic supplementary material The online version of this article (doi:10.1186/1742-4690-11-61) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, South Parks Road, Oxford OX1 3PS, UK.
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41
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Zehr SM, Roach RG, Haring D, Taylor J, Cameron FH, Yoder AD. Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center. Sci Data 2014; 1:140019. [PMID: 25977776 PMCID: PMC4322587 DOI: 10.1038/sdata.2014.19] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/18/2014] [Indexed: 11/26/2022] Open
Abstract
Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4,200 individuals from over 40 strepsirrhine primate taxa-the lemurs, lorises, and galagos. Here we present verified data for 3,627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated variables from which this summary table is built. Large sample sizes, longitudinal data that in many cases span an animal's entire life, exact dates of events, and large numbers of individuals from closely related yet biologically diverse primate taxa make these datasets unique. This single source for verified raw data and systematically compiled species values, particularly in combination with the availability of associated biological samples and the current live colony for research, will support future studies from an enormous spectrum of disciplines.
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Affiliation(s)
- Sarah M Zehr
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
- NESCent, Duke University, Durham, NC 27705, USA
| | - Richard G Roach
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - David Haring
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - Julie Taylor
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - Freda H Cameron
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - Anne D Yoder
- The Duke Lemur Center, Duke University, Durham, NC 27705, USA
- Department of Biology, Duke University, Durham, NC 27705, USA
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42
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Jones SM, Pearson J, DeWind NK, Paulsen D, Tenekedjieva AM, Brannon EM. Lemurs and macaques show similar numerical sensitivity. Anim Cogn 2014; 17:503-15. [PMID: 24068469 PMCID: PMC3966981 DOI: 10.1007/s10071-013-0682-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/07/2013] [Accepted: 09/09/2013] [Indexed: 01/29/2023]
Abstract
We investigated the precision of the approximate number system (ANS) in three lemur species (Lemur catta, Eulemur mongoz, and Eulemur macaco flavifrons), one Old World monkey species (Macaca mulatta) and humans (Homo sapiens). In Experiment 1, four individuals of each nonhuman primate species were trained to select the numerically larger of two visual arrays on a touchscreen. We estimated numerical acuity by modeling Weber fractions (w) and found quantitatively equivalent performance among all four nonhuman primate species. In Experiment 2, we tested adult humans in a similar procedure, and they outperformed the four nonhuman species but showed qualitatively similar performance. These results indicate that the ANS is conserved over the primate order.
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Affiliation(s)
- Sarah M Jones
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA,
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43
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Douzery EJP, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V. OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals. Mol Biol Evol 2014; 31:1923-8. [DOI: 10.1093/molbev/msu132] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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44
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Blair C, Heckman KL, Russell AL, Yoder AD. Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species. BMC Evol Biol 2014; 14:57. [PMID: 24661555 PMCID: PMC3987692 DOI: 10.1186/1471-2148-14-57] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/18/2014] [Indexed: 12/20/2022] Open
Abstract
Background Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned in size, with M. murinus showing a much more extensive range that marginally overlaps that of M. griseorufus. Given that these two species are sister taxa, the asymmetric but overlapping geographic ranges are consistent with a model of peripatric speciation. To test this hypothesis, we analyze DNA sequence data from four molecular markers using coalescent methods. If the peripatric speciation model is supported, we predict substantially greater genetic diversity in M. murinus, relative to M. griseorufus. Further, we expect a larger effective population size in M. murinus and in the common ancestor of the two species than in M. griseorufus, with a concomitant decrease in gene tree/species tree incongruence in the latter and weak signs of demographic expansion in M. murinus. Results Our results reject a model of peripatric divergence. Coalescent effective population size estimates were similar for both extant species and larger than that estimated for their most recent common ancestor. Gene tree results show similar levels of incomplete lineage sorting within species with respect to the species tree, and locus-specific estimates of genetic diversity are concordant for both species. Multilocus demographic analyses suggest range expansions for M. murinus, with this species also experiencing more recent population declines over the past 160 thousand years. Conclusions Results suggest that speciation occurred in allopatry from a common ancestor narrowly distributed throughout southwest Madagascar, with subsequent range expansion for M. murinus. Population decline in M. murinus is likely related to patterns of climate change in Madagascar throughout the Pleistocene, potentially exacerbated by continual anthropogenic perturbation. Genome-level data are needed to quantify the role of niche specialization and adaptation in shaping the current ranges of these species.
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Affiliation(s)
- Christopher Blair
- Department of Biology, Duke University, Box 90338, BioSci 130 Science Drive, Durham, NC 27708, USA.
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Baab KL, Perry JMG, Rohlf FJ, Jungers WL. PHYLOGENETIC, ECOLOGICAL, AND ALLOMETRIC CORRELATES OF CRANIAL SHAPE IN MALAGASY LEMURIFORMS. Evolution 2014; 68:1450-68. [DOI: 10.1111/evo.12361] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Karen L. Baab
- Department of Anthropology; Stony Brook University; Social and Behavioral Sciences Building; 5th Floor Stony Brook New York 11794
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
| | - Jonathan M. G. Perry
- Center for Functional Anatomy and Evolution; The Johns Hopkins University School of Medicine; Baltimore Maryland 21205
| | - F. James Rohlf
- Department of Ecology and Evolution; Stony Brook University; Stony Brook New York 11794
| | - William L. Jungers
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
- Department of Anatomical Sciences; Stony Brook University; Stony Brook New York 11794
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The ecology of spatial memory in four lemur species. Anim Cogn 2014; 17:947-61. [PMID: 24469310 DOI: 10.1007/s10071-014-0727-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/02/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Evolutionary theories suggest that ecology is a major factor shaping cognition in primates. However, there have been few systematic tests of spatial memory abilities involving multiple primate species. Here, we examine spatial memory skills in four strepsirrhine primates that vary in level of frugivory: ruffed lemurs (Varecia sp.), ring-tailed lemurs (Lemur catta), mongoose lemurs (Eulemur mongoz), and Coquerel's sifakas (Propithecus coquereli). We compare these species across three studies targeting different aspects of spatial memory: recall after a long-delay, learning mechanisms supporting memory and recall of multiple locations in a complex environment. We find that ruffed lemurs, the most frugivorous species, consistently showed more robust spatial memory than the other species across tasks-especially in comparison with sifakas, the most folivorous species. We discuss these results in terms of the importance of considering both ecological and social factors as complementary explanations for the evolution of primate cognitive skills.
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Affiliation(s)
- K. H. Dausmann
- Department of Animal Ecology and Conservation, Biocentre Grindel; University of Hamburg; Hamburg Germany
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Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2013; 31:817-31. [DOI: 10.1093/molbev/mst271] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Marivaux L, Ramdarshan A, Essid EM, Marzougui W, Ammar HK, Lebrun R, Marandat B, Merzeraud G, Tabuce R, Vianey-Liaud M. Djebelemur, a tiny pre-tooth-combed primate from the Eocene of Tunisia: a glimpse into the origin of crown strepsirhines. PLoS One 2013; 8:e80778. [PMID: 24324627 PMCID: PMC3851781 DOI: 10.1371/journal.pone.0080778] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/07/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Molecular clock estimates of crown strepsirhine origins generally advocate an ancient antiquity for Malagasy lemuriforms and Afro-Asian lorisiforms, near the onset of the Tertiary but most often extending back to the Late Cretaceous. Despite their inferred early origin, the subsequent evolutionary histories of both groups (except for the Malagasy aye-aye lineage) exhibit a vacuum of lineage diversification during most part of the Eocene, followed by a relative acceleration in diversification from the late Middle Eocene. This early evolutionary stasis was tentatively explained by the possibility of unrecorded lineage extinctions during the early Tertiary. However, this prevailing molecular view regarding the ancient origin and early diversification of crown strepsirhines must be viewed with skepticism due to the new but still scarce paleontological evidence gathered in recent years. METHODOLOGICAL/PRINCIPAL FINDINGS Here, we describe new fossils attributable to Djebelemur martinezi, a≈50 Ma primate from Tunisia (Djebel Chambi). This taxon was originally interpreted as a cercamoniine adapiform based on limited information from its lower dentition. The new fossils provide anatomical evidence demonstrating that Djebelemur was not an adapiform but clearly a distant relative of lemurs, lorises and galagos. Cranial, dental and postcranial remains indicate that this diminutive primate was likely nocturnal, predatory (primarily insectivorous), and engaged in a form of generalized arboreal quadrupedalism with frequent horizontal leaping. Djebelemur did not have an anterior lower dentition as specialized as that characterizing most crown strepsirhines (i.e., tooth-comb), but it clearly exhibited a transformed antemolar pattern representing an early stage of a crown strepsirhine-like adaptation ("pre-tooth-comb"). CONCLUSIONS/SIGNIFICANCE These new fossil data suggest that the differentiation of the tooth-comb must postdate the djebelemurid divergence, a view which hence constrains the timing of crown strepsirhine origins to the Middle Eocene, and then precludes the existence of unrecorded lineage extinctions of tooth-combed primates during the earliest Tertiary.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
| | - Anusha Ramdarshan
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
- Section of Vertebrate Paleontology, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, United States of America
| | | | | | | | - Renaud Lebrun
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
| | - Bernard Marandat
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
| | - Gilles Merzeraud
- Géosciences Montpellier (UMR-CNRS 5243), Université Montpellier 2, Montpellier, France
| | - Rodolphe Tabuce
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
| | - Monique Vianey-Liaud
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR-CNRS 5554), Université Montpellier 2, Montpellier, France
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