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Nakamura K, Kanaya M, Matsushima D, Dunn JC, Hirabayashi H, Sato K, Tokuda IT, Nishimura T. Twin vocal folds as a novel evolutionary adaptation for vocal communications in lemurs. Sci Rep 2024; 14:3631. [PMID: 38351102 PMCID: PMC10864409 DOI: 10.1038/s41598-024-54172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Primates have varied vocal repertoires to communicate with conspecifics and sometimes other species. The larynx has a central role in vocal source generation, where a pair of vocal folds vibrates to modify the air flow. Here, we show that Madagascan lemurs have a unique additional pair of folds in the vestibular region, parallel to the vocal folds. The additional fold has a rigid body of a vocal muscle branch and it is covered by a stratified squamous epithelium, equal to those of the vocal fold. Such anatomical features support the hypothesis that it also vibrates in a manner like the vibrations that occur in the vocal folds. To examine the acoustic function of the two pairs of folds, we made a silicone compound model to demonstrate that they can simultaneously vibrate to lower the fundamental frequency and increase vocal efficiency. Similar acoustic effects are achieved using different features of the larynx for the other primates, e.g., by vibrating multiple sets of ventricular folds in several species and further by an evolutionary modification of enlarged larynx in howler monkeys. Our multidisciplinary approaches found that these functions were acquired through a unique evolutionary adaptation of the twin vocal folds in Madagascan lemurs.
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Affiliation(s)
- Kanta Nakamura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
| | - Mayuka Kanaya
- College of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Daisuke Matsushima
- College of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Jacob C Dunn
- Behavioural Ecology Research Group, Anglia Ruskin University, Cambridge, UK
- Biological Anthropology, The University of Cambridge, Cambridge, UK
- Department of Cognitive Biology, University of Vienna, Vienna, Austria
| | | | - Kiminori Sato
- Department of Otolaryngology-Head and Neck Surgery, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Isao T Tokuda
- College of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Nishimura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan.
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2
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Lyčka M, Bubeník M, Závodník M, Peska V, Fajkus P, Demko M, Fajkus J, Fojtová M. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Res 2024; 52:D311-D321. [PMID: 37602392 PMCID: PMC10767889 DOI: 10.1093/nar/gkad672] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023] Open
Abstract
Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, 'Telomerase database' and 'Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Bubeník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Závodník
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Faculty of Informatics, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
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Winn JC, Maduna SN, Bester-van der Merwe AE. A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics 2024; 116:110771. [PMID: 38147941 DOI: 10.1016/j.ygeno.2023.110771] [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: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
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Affiliation(s)
- Jessica C Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa
| | - Simo N Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
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Miarisoa JE, Raveloson H, Randrianambinina B, Couette S. Deciphering the mandibular shape variation in a group of Malagasy primates using Fourier outline analysis. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:372-387. [PMID: 37676062 DOI: 10.1002/ajpa.24832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVES Among living Malagasy primates, the family Lemuridae has previously been recognized as presenting a higher mandibular morphological variation than other families. We conducted a quantitative analysis of mandibular size and shape within the five genera (Lemur, Eulemur, Hapalemur, Prolemur, and Varecia) associated with a set of covariables that could explain this variation. MATERIALS AND METHODS We used Fourier outline analysis on the left hemimandible of 182 specimens covering the Lemuridae family. The influence of the phylogeny but also seven covariables (genus, diet, sex, sexual behavior, mating system, ecoregion, and forest type) on mandibular variation was examined using multivariate statistics and model selection. RESULTS Our results indicate that the high level of morphological variation within the family, associated with a phylogenetic effect and differences in diet, is due to a strong distinction between the genera Prolemur and Hapalemur and the other genera of the family. A second analysis, correcting this strong effect, indicates that mandibular shape variation is influenced not only by the phylogeny and the diet but by a combination of all the covariables. DISCUSSION The analysis of morphological variation is a powerful tool with major applications, both for the estimation of biological diversity and for the understanding of the fundamental parameters of species' ecology. Our work indicates that, if mandibular shape variation is mainly driven by dietary adaptation, other variables describing ecology and habitat should be considered and taken into account for an integrative understanding of species resources and the establishment of conservation measures.
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Affiliation(s)
- Jeanne Emma Miarisoa
- École Doctorale Ecosystèmes Naturels, (EDEN), University of Mahajanga, Mahajanga, BP, Madagascar
- UMR CNRS/uB/EPHE 6282 Biogéosciences, Dijon, France
- École Pratique des Hautes Etudes, PSL, Paris, France
| | - Herimalala Raveloson
- École Doctorale Ecosystèmes Naturels, (EDEN), University of Mahajanga, Mahajanga, BP, Madagascar
| | | | - Sébastien Couette
- UMR CNRS/uB/EPHE 6282 Biogéosciences, Dijon, France
- École Pratique des Hautes Etudes, PSL, Paris, France
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Ali JR, Hedges SB. The colonisation of Madagascar by land-bound vertebrates. Biol Rev Camb Philos Soc 2023; 98:1583-1606. [PMID: 37142264 DOI: 10.1111/brv.12966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
Despite discussions extending back almost 160 years, the means by which Madagascar's iconic land vertebrates arrived on the island remains the focus of active debate. Three options have been considered: vicariance, range expansion across land bridges, and dispersal over water. The first assumes that a group (clade/lineage) occupied the island when it was connected with the other Gondwana landmasses in the Mesozoic. Causeways to Africa do not exist today, but have been proposed by some researchers for various times in the Cenozoic. Over-water dispersal could be from rafting on floating vegetation (flotsam) or by swimming/drifting. A recent appraisal of the geological data supported the idea of vicariance, but found nothing to justify the notion of past causeways. Here we review the biological evidence for the mechanisms that explain the origins of 28 of Madagascar's land vertebrate clades [two other lineages (the geckos Geckolepis and Paragehyra) could not be included in the analysis due to phylogenetic uncertainties]. The podocnemid turtles and typhlopoid snakes are conspicuous for they appear to have arisen through a deep-time vicariance event. The two options for the remaining 26 (16 reptile, five land-bound-mammal, and five amphibian), which arrived between the latest Cretaceous and the present, are dispersal across land bridges or over water. As these would produce very different temporal influx patterns, we assembled and analysed published arrival times for each of the groups. For all, a 'colonisation interval' was generated that was bracketed by its 'stem-old' and 'crown-young' tree-node ages; in two instances, the ranges were refined using palaeontological data. The synthesis of these intervals for all clades, which we term a colonisation profile, has a distinctive shape that can be compared, statistically, to various models, including those that assume the arrivals were focused in time. The analysis leads us to reject the various land bridge models (which would show temporal concentrations) and instead supports the idea of dispersal over water (temporally random). Therefore, the biological evidence is now in agreement with the geological evidence, as well as the filtered taxonomic composition of the fauna, in supporting over-water dispersal as the mechanism that explains all but two of Madagascar's land-vertebrate groups.
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Affiliation(s)
- Jason R Ali
- Department of Earth Sciences, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - S Blair Hedges
- Center for Biodiversity, Temple University, 1925 N 12th Street, Suite 502, Philadelphia, PA, 19122, USA
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Kessler SE, Tsangaras K, Rasoloharijaona S, Radespiel U, Greenwood AD. Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression. Virus Evol 2022; 9:veac117. [PMID: 36632481 PMCID: PMC9825726 DOI: 10.1093/ve/veac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Madagascar's flora and fauna have evolved in relative isolation since the island split from the African and Indian continents. When the last common ancestors of lemurs left Africa between 40 and 70 million years ago, they carried a subset of the viral diversity of the mainland population within them, which continued to evolve throughout the lemur radiation. Relative to other primate radiations, we know very little about the past or present viral diversity of lemurs, particularly mouse lemurs. Using high-throughput sequencing, we identified two gammaretroviruses and three betaretroviruses in the genomes of four species of wild mouse lemurs. The two gammaretroviruses and two betaretroviruses have not previously been described. One betaretrovirus was previously identified. All identified viruses are present in both Lorisiformes and Lemuriformes but absent from haplorrhine primates. The estimated ages of these viruses are consistent with the estimated divergence dates of the host lineages, suggesting they colonized the lemur genome after the Haplorrhine-Strepsirrhine split, but before the Lorisiformes-Lemuriformes split and before the colonization of Madagascar. The viral phylogenies connect multiple lineages of retroviruses from non-lemur and non-Madagascar-native species, suggesting substantial cross-species transmission occurred deep in the primate clade prior to its geographic dispersal. These phylogenies provide novel insights into known retroviral clades. They suggest that the origin of gammaretroviruses in rodents or bats may be premature and that the Jaagsiekte sheep virus clade may be older and more broadly distributed among mammals than previously thought.
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Affiliation(s)
| | - Kyriakos Tsangaras
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin 10315, Germany,Department of Life and Health Sciences, University of Nicosia, 46 Makedonitissas Avenue, CY-2417, P.O. Box 24005, Nicosia, CY-1700, Cyprus
| | - Solofonirina Rasoloharijaona
- Faculty of Science, Technology and Environment, University of Mahajanga, 5 Georges V Street - Building KAKAL Mahajanga Be - Po. Box 652 , Mahajanga 401, Madagascar
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Buenteweg 17, Hannover 30559, Germany
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Crouch NMA, Jablonski D. Is species richness mediated by functional and genetic divergence? A global analysis in birds. Funct Ecol 2022; 37:125-138. [PMID: 37064506 PMCID: PMC10086807 DOI: 10.1111/1365-2435.14153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.
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Affiliation(s)
- Nicholas M. A. Crouch
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
| | - David Jablonski
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
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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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Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka. Genes (Basel) 2022; 13:genes13061026. [PMID: 35741788 PMCID: PMC9223071 DOI: 10.3390/genes13061026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken’s (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier’s (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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Valente D, Miaretsoa L, Anania A, Costa F, Mascaro A, Raimondi T, De Gregorio C, Torti V, Friard O, Ratsimbazafy J, Giacoma C, Gamba M. Comparative Analysis of the Vocal Repertoires of the Indri (Indri indri) and the Diademed Sifaka (Propithecus diadema). INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00287-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
AbstractStrepsirrhine vocalisations are extraordinarily diverse and cross-species comparisons are needed to explore how this variability evolved. We contributed to the investigation of primate acoustic diversity by comparing the vocal repertoire of two sympatric lemur species, Propithecus diadema and Indri indri. These diurnal species belong to the same taxonomic family and have similar activity patterns but different social structures. These features make them excellent candidates for an investigation of the phylogenetic, environmental, and social influence on primate vocal behavior. We recorded 3 P. diadema groups in 2014 and 2016. From 1,872 recordings we selected and assigned 3814 calls to 9 a priori call types, on the basis of their acoustic structure. We implemented a reproducible technique performing an acoustic feature extraction relying on frequency bins, t-SNE data reduction, and a hard-clustering analysis. We first quantified the vocal repertoire of P. diadema, finding consistent results for the 9 putatively identified call types. When comparing this repertoire with a previously published repertoire of I. indri, we found highly species-specific repertoires, with only 2% of the calls misclassified by species identity. The loud calls of the two species were very distinct, while the low-frequency calls were more similar. Our results pinpoint the role of phylogenetic history, social and environmental features on the evolution of communicative systems and contribute to a deeper understanding of the evolutionary roots of primate vocal differentiation. We conclude by arguing that standardized and reproducible techniques, like the one we employed, allow robust comparisons and should be prioritized in the future.
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Tinsman J, Volampeno S, Ganas-Swaray J, Gann D, Andrianirina N, Chamizo M, Ralazampirenena C, Ranaivoarisoa JF, Ravaoarisoa H, Rivero J, Zamora A, Gomes CM. Habitat use by the island lemurs of Nosy Be, Madagascar. Am J Primatol 2022; 84:e23362. [PMID: 35098568 DOI: 10.1002/ajp.23362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 01/01/2023]
Abstract
Madagascar's lemurs are threatened by forest loss, fragmentation, and degradation. Many species use flexible behaviors to survive in degraded habitat, but their ability to persist in very small areas may be limited. Insular lemurs, like those found on Nosy Be, an island off the northwestern coast of Madagascar, are at heightened risk of sudden population declines and extirpation. Nosy Be is home to two Critically Endangered species-the endemic Nosy Be sportive lemur (Lepilemur tymerlachsoni) and Claire's mouse lemur (Microcebus mamiratra)-as well as the Endangered black lemur (Eulemur macaco). Most of the remaining forest on Nosy Be is protected by the 862-ha Lokobe National Park. To document how Nosy Be lemurs use their restricted habitat, we conducted vegetation and reconnaissance surveys on 53 transects in and around Lokobe. We collected data on tree size, canopy cover, understory visibility, and elevation for 248 lemur sightings. We used a spatially explicit, multi-species occupancy model to investigate which forest-structure variables are important to lemurs. Our results represent some of the first data on habitat use by insular lemurs. Black lemurs preferred significantly larger trees and areas with less dense understory. They also occurred significantly less outside of Lokobe National Park, even when accounting for sampling effort and geography. The distributions of the sportive and mouse lemurs were not related to the forest structure variables we documented, but they did negatively predict each other-perhaps because their habitat requirements differ. These results also underscore the importance of the national park to protecting the black lemur population on Nosy Be and raise questions about what factors do influence the distribution of Nosy Be's smaller lemurs. Close monitoring is needed to prevent these populations and the ecosystem services they provide from disappearing, as have other island lemurs.
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Affiliation(s)
- Jen Tinsman
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Center for Tropical Research, Institute of the Environment & Sustainability, University of California, Los Angeles, USA
| | | | | | - Daniel Gann
- Department of Biology, FIU, Miami, Florida, USA
| | - Natacha Andrianirina
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Department of Anthropobiology and Sustainable Development, Université d'Antananarivo, Antananarivo, Madagascar
| | - Madison Chamizo
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA
| | - Claude Ralazampirenena
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Ministère de l'Environnement et du Développement Durable, Antananarivo, Madagascar
| | - Jean F Ranaivoarisoa
- Department of Anthropobiology and Sustainable Development, Université d'Antananarivo, Antananarivo, Madagascar
| | - Hasina Ravaoarisoa
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Department of Anthropobiology and Sustainable Development, Université d'Antananarivo, Antananarivo, Madagascar
| | - Josie Rivero
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Department of Ecology & Environmental Studies, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Andrew Zamora
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA.,Department of Anthropology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Cristina M Gomes
- Tropical Conservation Institute, Institute of Environment, Florida International University, Miami, Florida, USA
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13
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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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14
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Amorim CEG, Dasari M, Durgavich L, Hinde K, Kissel M, Lewton KL, Loewen T. Integrative approaches to dispersing science: A case study of March Mammal Madness. Am J Hum Biol 2021; 34 Suppl 1:e23659. [PMID: 34358377 DOI: 10.1002/ajhb.23659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Public engagement is increasingly viewed as an important pillar of scientific scholarship. For early career and established scholars, navigating the mosaic landscape of public education and science communication, noted for rapid "ecological" succession, can be daunting. Moreover, academics are characterized by diverse skills, motivations, values, positionalities, and temperaments that may differentially incline individuals to particular public translation activities. METHODS Here we briefly contextualize engagement activities within a scholarly portfolio, describe the use of one public education program-March Mammal Madness (MMM)- to highlight approaches to science communication, and explore essential elements and practical considerations for creating and sustaining outreach pursuits in tandem with other scholarly activities. RESULTS MMM, an annual simulated tournament of living and fossil animal taxa, has reached hundreds of thousands of learners since 2013. This program has provided a platform to communicate research findings from biology and anthropology and showcase numerous scholars in these fields. MMM has leveraged tournament devices to intentionally address topics of climate change, capitalist environmental degradation, academic sexism, and racist settler-colonialism. The tournament, however, has also perpetuated implicit biases that need disrupting. CONCLUSIONS By embracing reflexive, self-interrogative, and growth attitudes, the tournament organizers iteratively refine and improve this public science education program to better align our activities with our values and goals. Our experiences with MMM suggest that dispersing science is most sustainable when we combine ancestral adaptations for cooperation, community, and storytelling with good-natured competition in the context of shared experiences and shared values.
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Affiliation(s)
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lara Durgavich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Katie Hinde
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Marc Kissel
- Department of Anthropology, Appalachian State University, Boone, North Carolina, USA
| | - Kristi L Lewton
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tisa Loewen
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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15
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Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map. Proc Natl Acad Sci U S A 2021; 118:2110218118. [PMID: 34301878 DOI: 10.1073/pnas.2110218118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Marciniak S, Mughal MR, Godfrey LR, Bankoff RJ, Randrianatoandro H, Crowley BE, Bergey CM, Muldoon KM, Randrianasy J, Raharivololona BM, Schuster SC, Malhi RS, Yoder AD, Louis EE, Kistler L, Perry GH. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. Proc Natl Acad Sci U S A 2021; 118:e2022117118. [PMID: 34162703 PMCID: PMC8255780 DOI: 10.1073/pnas.2022117118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Mehreen R Mughal
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
| | - Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003
| | - Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Heritiana Randrianatoandro
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brooke E Crowley
- Department of Geology, University of Cincinnati, Cincinnati, OH 45220
- Department of Anthropology, University of Cincinnati, Cincinnati, OH 45220
| | - Christina M Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Rutgers University, New Brunswick, NJ 08854
| | | | - Jeannot Randrianasy
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brigitte M Raharivololona
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 639798
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801
- Department of Ecology, Evolution and Behavior, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Edward E Louis
- Department of Conservation Genetics, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107;
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560;
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802;
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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17
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Hekkala E, Gatesy J, Narechania A, Meredith R, Russello M, Aardema ML, Jensen E, Montanari S, Brochu C, Norell M, Amato G. Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus. Commun Biol 2021; 4:505. [PMID: 33907305 PMCID: PMC8079395 DOI: 10.1038/s42003-021-02017-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.
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Affiliation(s)
- E Hekkala
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
- American Museum of Natural History, New York, NY, USA.
| | - J Gatesy
- American Museum of Natural History, New York, NY, USA
| | - A Narechania
- American Museum of Natural History, New York, NY, USA
| | - R Meredith
- American Museum of Natural History, New York, NY, USA
- Montclair State University, Montclair, NJ, USA
| | - M Russello
- University of British Columbia, Department of Biology, Kelowna, BC, Canada
| | - M L Aardema
- American Museum of Natural History, New York, NY, USA
- Montclair State University, Montclair, NJ, USA
| | - E Jensen
- University of British Columbia, Department of Biology, Kelowna, BC, Canada
- Newcastle University, School of Natural and Environmental Sciences Ecology Group, Newcastle, UK
| | - S Montanari
- American Museum of Natural History, New York, NY, USA
| | - C Brochu
- University of Iowa, Department of Geosciences, Iowa City, IA, USA
| | - M Norell
- American Museum of Natural History, New York, NY, USA
| | - G Amato
- American Museum of Natural History, New York, NY, USA
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18
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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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19
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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20
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Godfrey LR, Samonds KE, Baldwin JW, Sutherland MR, Kamilar JM, Allfisher KL. Mid-Cenozoic climate change, extinction, and faunal turnover in Madagascar, and their bearing on the evolution of lemurs. BMC Evol Biol 2020; 20:97. [PMID: 32770933 PMCID: PMC7414565 DOI: 10.1186/s12862-020-01628-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/18/2020] [Indexed: 01/16/2023] Open
Abstract
Background Was there a mid-Cenozoic vertebrate extinction and recovery event in Madagascar and, if so, what are its implications for the evolution of lemurs? The near lack of an early and mid-Cenozoic fossil record on Madagascar has inhibited direct testing of any such hypotheses. We compare the terrestrial vertebrate fauna of Madagascar in the Holocene to that of early Cenozoic continental Africa to shed light on the probability of a major mid-Cenozoic lemur extinction event, followed by an “adaptive radiation” or recovery. We also use multiple analytic approaches to test competing models of lemur diversification and the null hypothesis that no unusual mid-Cenozoic extinction of lemurs occurred. Results Comparisons of the terrestrial vertebrate faunas of the early Cenozoic on continental Africa and Holocene on Madagascar support the inference that Madagascar suffered a major mid-Cenozoic extinction event. Evolutionary modeling offers some corroboration, although the level of support varies by phylogeny and model used. Using the lemur phylogeny and divergence dates generated by Kistler and colleagues, RPANDA and TESS offer moderate support for the occurrence of unusual extinction at or near the Eocene-Oligocene (E-O) boundary (34 Ma). TreePar, operating under the condition of obligate mass extinction, found peak diversification at 31 Ma, and low probability of survival of prior lineages. Extinction at the E-O boundary received greater support than other candidate extinctions or the null hypothesis of no major extinction. Using the lemur phylogeny and divergence dates generated by Herrera & Dàvalos, evidence for large-scale extinction diminishes and its most likely timing shifts to before 40 Ma, which fails to conform to global expectations. Conclusions While support for large-scale mid-Cenozoic lemur extinction on Madagascar based on phylogenetic modeling is inconclusive, the African fossil record does provide indirect support. Furthermore, a major extinction and recovery of lemuriforms during the Eocene-Oligocene transition (EOT) would coincide with other major vertebrate extinctions in North America, Europe, and Africa. It would suggest that Madagascar’s lemurs were impacted by the climate shift from “greenhouse” to “ice-house” conditions that occurred at that time. This could, in turn, help to explain some of the peculiar characteristics of the lemuriform clade.
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Affiliation(s)
- Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.
| | - Karen E Samonds
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Justin W Baldwin
- Department of Public Health, School of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA.,Present Address: Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Michael R Sutherland
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jason M Kamilar
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA
| | - Kristen L Allfisher
- Department of Anthropology, University of Massachusetts, 217 Machmer Hall, 240 Hicks Way, Amherst, MA, 01003, USA.,Present Address: USDA, APHIS, Riverdale, MD, 20737, USA
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21
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Chandrashekar A, Knierim JA, Khan S, Raboin DL, Venkatesh S, Clarke TA, Cuozzo FP, LaFleur M, Lawler RR, Parga JA, Rasamimanana HR, Reuter KE, Sauther ML, Baden AL. Genetic population structure of endangered ring-tailed lemurs ( Lemur catta) from nine sites in southern Madagascar. Ecol Evol 2020; 10:8030-8043. [PMID: 32788959 PMCID: PMC7417237 DOI: 10.1002/ece3.6337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 03/31/2020] [Accepted: 04/09/2020] [Indexed: 11/06/2022] Open
Abstract
Madagascar's ring-tailed lemurs (Lemur catta) are experiencing rapid population declines due to ongoing habitat loss and fragmentation, as well as increasing exploitation for bushmeat and the illegal pet trade. Despite being the focus of extensive and ongoing behavioral studies, there is comparatively little known about the genetic population structuring of the species. Here, we present the most comprehensive population genetic analysis of ring-tailed lemurs to date from across their likely remaining geographic range. We assessed levels of genetic diversity and population genetic structure using multilocus genotypes for 106 adult individuals from nine geographically representative localities. Population structure and F ST analyses revealed moderate genetic differentiation with localities being geographically partitioned into northern, southern, western and also potentially central clusters. Overall genetic diversity, in terms of allelic richness and observed heterozygosity, was high in the species (AR = 4.74, H O = 0.811). In fact, it is the highest among all published lemur estimates to date. While these results are encouraging, ring-tailed lemurs are currently affected by ongoing habitat fragmentation and occur at lower densities in poorer quality habitats. The effects of continued isolation and fragmentation, coupled with climate-driven environmental instability, will therefore likely impede the long-term viability of the species.
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Affiliation(s)
- Aparna Chandrashekar
- Department of AnthropologyHunter College of the City University of New YorkNew YorkNYUSA
- Present address:
San Diego Zoo Global Institute for Conservation ResearchSan DiegoCAUSA
| | - Jessica A. Knierim
- Animal Behavior and Conservation ProgramDepartment of PsychologyHunter College of the City University of New YorkNew YorkNYUSA
- Present address:
Wildlife AllianceNew YorkNYUSA
| | - Sohail Khan
- Department of AnthropologyHunter College of the City University of New YorkNew YorkNYUSA
| | - Dominique L. Raboin
- Animal Behavior and Conservation ProgramDepartment of PsychologyHunter College of the City University of New YorkNew YorkNYUSA
- Present address:
Rutgers UniversityNew BrunswickNJUSA
| | - Sateesh Venkatesh
- Animal Behavior and Conservation ProgramDepartment of PsychologyHunter College of the City University of New YorkNew YorkNYUSA
| | - Tara A. Clarke
- Department of Sociology and AnthropologyNorth Carolina State UniversityRaleighNCUSA
| | | | - Marni LaFleur
- Department of AnthropologyUniversity of San DiegoSan DiegoCAUSA
- Lemur Love, Inc.San DiegoCAUSA
| | - Richard R. Lawler
- Department of Sociology and AnthropologyJames Madison UniversityHarrisonburgVAUSA
| | - Joyce A. Parga
- Department of AnthropologyCalifornia State University‐Los AngelesLos AngelesCAUSA
| | | | - Kim E. Reuter
- Pet Lemur SurveyHoused by the University of UtahSalt Lake CityUTUSA
| | | | - Andrea L. Baden
- Department of AnthropologyHunter College of the City University of New YorkNew YorkNYUSA
- Department of AnthropologyThe Graduate Center of the City University of New YorkNew YorkNYUSA
- The New York Consortium in Evolutionary Primatology (NYCEP)New YorkNYUSA
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22
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Andrews C, Masters JC, Génin F, Couette S. The evolution of palate shape in the Lepilemur-Cheirogaleidae clade (Primates: Strepsirrhini). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:307-321. [PMID: 32666552 DOI: 10.1002/ajpa.24093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 11/10/2022]
Abstract
OBJECTIVES Phylogenies consistently group the folivorous Lepilemur species with the small-bodied insectivorous-frugivorous cheirogaleids. Juvenile lepilemurs and adult cheirogaleids share allometries in most aspects of skull morphology, except the palate. We investigated potential influences on palate shape in these taxa and several outgroups using geometric morphometrics. MATERIALS AND METHODS Our sample included representatives of four extant strepsirrhine families, Cheirogaleidae (including Lepilemurinae), Lemuridae, Indriidae, and Galagidae, and one subfossil Megaladapis. Our dataset comprised 32 landmarks collected from 397 specimens representing 15 genera and 28 species, and was analyzed using generalized procrustes analyses and between group principal component analysis. We explored the influence of size, phylogeny, diet, and the propagation of loud vocalizations on palate shape. RESULTS While congeneric species clustered within the morphospace, the phylomorphospace did not mirror molecular phylogenetic hypotheses of higher-order relationships. Four palate forms were distinguished within the Cheirogaleidae. Diet, strongly linked to body size, had the single greatest influence on palate shape. The production of long-distance advertisement calls was most often associated with positive scores on the PC1 axis. DISCUSSION Our results suggest that the extensive variation in palate shape among Cheirogaleidae is related to dietary shifts that accompanied changes in body size during the clade's radiation. Molecular phylogenies indicate that cheirogaleid diversification involved repeated dwarfing events, which in turn drove dietary shifts from ancestral folivory-frugivory to frugivory, gummivory, and faunivory in the descendant species. The elongated Lepilemur palate is probably related to accelerated eruption of the cheek teeth to render juveniles competent to shear leaves upon weaning.
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Affiliation(s)
- Curswan Andrews
- Centre for African Conservation Ecology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,African Primate Initiative for Ecology and Speciation (APIES), Earth Stewardship Science Research Institute, Nelson Mandela University, Port Elizabeth, South Africa.,APIES, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Judith C Masters
- APIES, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa.,Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Fabien Génin
- African Primate Initiative for Ecology and Speciation (APIES), Earth Stewardship Science Research Institute, Nelson Mandela University, Port Elizabeth, South Africa
| | - Sébastien Couette
- EPHE, PSL Paris Université, Paris, France.,UMR CNRS 6282 Biogéosciences, Université de Bourgogne, Dijon, France
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23
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Branching out: what omics can tell us about primate evolution. Curr Opin Genet Dev 2020; 62:65-71. [DOI: 10.1016/j.gde.2020.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022]
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24
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Bornbusch SL, Greene LK, McKenney EA, Volkoff SJ, Midani FS, Joseph G, Gerhard WA, Iloghalu U, Granek J, Gunsch CK. A comparative study of gut microbiomes in captive nocturnal strepsirrhines. Am J Primatol 2019; 81:e22986. [PMID: 31081142 DOI: 10.1002/ajp.22986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 11/10/2022]
Abstract
Feeding strategy and diet are increasingly recognized for their roles in governing primate gut microbiome (GMB) composition. Whereas feeding strategy reflects evolutionary adaptations to a host's environment, diet is a more proximate measure of food intake. Host phylogeny, which is intertwined with feeding strategy, is an additional, and often confounding factor that shapes GMBs across host lineages. Nocturnal strepsirrhines are an intriguing and underutilized group in which to examine the links between these three factors and GMB composition. Here, we compare GMB composition in four species of captive, nocturnal strepsirrhines with varying feeding strategies and phylogenetic relationships, but nearly identical diets. We use 16S rRNA sequences to determine gut bacterial composition. Despite similar husbandry conditions, including diet, we find that GMB composition varies significantly across host species and is linked to host feeding strategy and phylogeny. The GMBs of the omnivorous and the frugivorous species were significantly more diverse than were those of the insectivorous and exudativorous species. Across all hosts, GMBs were enriched for bacterial taxa associated with the macronutrient resources linked to the host's respective feeding strategy. Ultimately, the reported variation in microbiome composition suggests that the impacts of captivity and concurrent diet do not overshadow patterns of feeding strategy and phylogeny. As our understanding of primate GMBs progresses, populations of captive primates can provide insight into the evolution of host-microbe relationships, as well as inform future captive management protocols that enhance primate health and conservation.
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Affiliation(s)
- Sally L Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Lydia K Greene
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,University Program in Ecology, Duke University, Durham, North Carolina
| | - Erin A McKenney
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Savannah J Volkoff
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina
| | - Firas S Midani
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Gail Joseph
- Department of Energy and Environmental Systems, North Carolina Agricultural and Technical State University, Greensboro, North Carolina
| | - William A Gerhard
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina
| | - Uchenna Iloghalu
- Department of Applied Science and Technology, North Carolina Agricultural and Technical State University, Greensboro, North Carolina
| | - Joshua Granek
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina
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25
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Delsuc F, Kuch M, Gibb GC, Hughes J, Szpak P, Southon J, Enk J, Duggan AT, Poinar HN. Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii) using mitogenomic and nuclear exon data. Proc Biol Sci 2019; 285:rspb.2018.0214. [PMID: 29769358 PMCID: PMC5966596 DOI: 10.1098/rspb.2018.0214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/16/2018] [Indexed: 01/18/2023] Open
Abstract
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kb of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths, from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloth lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole-genome sequencing of this emblematic extinct taxon.
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Affiliation(s)
- Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gillian C Gibb
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Jonathan Hughes
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, ON, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, CA, USA
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.,MYcroarray, Ann Arbor, MI, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
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26
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Sehner S, Fichtel C, Kappeler PM. Primate tails: Ancestral state reconstruction and determinants of interspecific variation in primate tail length. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:750-759. [PMID: 30341951 DOI: 10.1002/ajpa.23703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/30/2018] [Accepted: 08/04/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Living primates vary considerably in tail length-body size relation, ranging from tailless species to those where the tail is more than twice as long as the body. Because the general pattern and determinants of tail evolution remain incompletely known, we reconstructed evolutionary changes in relative tail length across all primates and sought to explain interspecific variation in this trait. METHODS We combined data on tail length, head-body length, intermembral index (IMI), habitat use, locomotion type, and range latitude for 340 species from published sources. We reconstructed the evolution of relative tail length to identify all independent cases of regime shifts on a primate phylogeny, using several methods based on Ornstein-Uhlenbeck (OU) models. Accounting for phylogeny, we also examined the effects of habitat, locomotion type, distance from the equator and IMI on interspecific variation in tail length-body size relation. RESULTS Primate tail length is not sexually dimorphic. A phylogenetic reconstruction allowing multiple optima explains the observed regime shifts best. During the evolutionary history of primates, relative tail length changed 50 times under an OU model. Specifically, relative tail length increased 26 and decreased 24 times. Most of these changes occurred among Old World primates. Among the variables tested here, interspecific variation in IMI and the difference between leaping and non-leaping locomotion explained interspecific variation in relative tail length: Evolutionary decreases in relative tail length are generally associated with an increase in IMI and an absence of leaping behavior. CONCLUSIONS Regime shifts for relative tail length in living primates occurred in concert with fundamental changes in IMI and a change from leaping to non-leaping locomotion, or vice versa. Exceptions from this general pattern are linked to the presence of a prehensile tail or specialized foraging strategies. Thus, the primate tail appears to have evolved in functional coordination with limb proportions, presumably to assist body balance.
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Affiliation(s)
- Sandro Sehner
- Department of Anthropology/Sociobiology, University of Göttingen, Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Peter M Kappeler
- Department of Anthropology/Sociobiology, University of Göttingen, Göttingen, Germany
- Behavioral Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
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27
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Monson TA, Hlusko LJ. Breaking the rules: Phylogeny, not life history, explains dental eruption sequence in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:217-233. [DOI: 10.1002/ajpa.23618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tesla A. Monson
- Department of Integrative Biology; University of California; Berkeley California 94720
- Museum of Vertebrate Zoology, Department of Integrative Biology; University of California; Berkeley California 94720
- Human Evolution Research Center, Department of Integrative Biology; University of California; Berkeley California 94720
| | - Leslea J. Hlusko
- Department of Integrative Biology; University of California; Berkeley California 94720
- Museum of Vertebrate Zoology, Department of Integrative Biology; University of California; Berkeley California 94720
- Human Evolution Research Center, Department of Integrative Biology; University of California; Berkeley California 94720
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28
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Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE. An environmental DNA sampling method for aye-ayes from their feeding traces. Ecol Evol 2018; 8:9229-9240. [PMID: 30377496 PMCID: PMC6194247 DOI: 10.1002/ece3.4341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye's mitochondrial genome and used these to isolate aye-aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye's geographic range that had not been sampled previously. Our method demonstrates the application of next-generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-ayes.
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Affiliation(s)
- Megan L. Aylward
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Alexis P. Sullivan
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
| | - George H. Perry
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
- Department of AnthropologyPennsylvania State UniversityState CollegePennsylvania
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Edward E. Louis
- Grewcock Center for Conservation and ResearchOmaha's Henry Doorly Zoo and AquariumOmahaNebraska
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29
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Gunnell GF, Boyer DM, Friscia AR, Heritage S, Manthi FK, Miller ER, Sallam HM, Simmons NB, Stevens NJ, Seiffert ER. Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar's aye-aye. Nat Commun 2018; 9:3193. [PMID: 30131571 PMCID: PMC6104046 DOI: 10.1038/s41467-018-05648-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 07/15/2018] [Indexed: 01/05/2023] Open
Abstract
In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange mammal is a strepsirrhine primate as originally suggested by Simpson. Moreover, our phylogenetic analyses support the recognition of Propotto, together with late Eocene Plesiopithecus from Egypt, as African stem chiromyiform lemurs that are exclusively related to the extant aye-aye (Daubentonia) from Madagascar. Our results challenge the long-held view that all lemurs are descended from a single ancient colonization of Madagascar, and present an intriguing alternative scenario in which two lemur lineages dispersed from Africa to Madagascar independently, possibly during the later Cenozoic.
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Affiliation(s)
- Gregg F Gunnell
- Division of Fossil Primates, Duke Lemur Center, Durham, NC, 27705, USA
| | - Doug M Boyer
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27705, USA
| | - Anthony R Friscia
- Department of Integrative Biology & Physiology, University of California - Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven Heritage
- Division of Fossil Primates, Duke Lemur Center, Durham, NC, 27705, USA
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Fredrick Kyalo Manthi
- Department of Earth Sciences, National Museums of Kenya, Museum Hill, P.O. Box 40658-00100, Nairobi, 00100, Kenya
| | - Ellen R Miller
- Department of Anthropology, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Hesham M Sallam
- Mansoura University Vertebrate Paleontology Center (MUVP), Department of Geology, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Nancy J Stevens
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA
- Center for Ecology and Evolutionary Studies, Ohio University, Athens, OH, 45701, USA
| | - Erik R Seiffert
- Department of Integrative Anatomical Sciences, Keck School of Medicine of USC, University of Southern California, 1333 San Pablo Street, BMT 406, Los Angeles, CA, 90033, USA.
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA.
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30
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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31
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Jacobs RL, MacFie TS, Spriggs AN, Baden AL, Morelli TL, Irwin MT, Lawler RR, Pastorini J, Mayor M, Lei R, Culligan R, Hawkins MTR, Kappeler PM, Wright PC, Louis EE, Mundy NI, Bradley BJ. Novel opsin gene variation in large-bodied, diurnal lemurs. Biol Lett 2017; 13:rsbl.2017.0050. [PMID: 28275167 DOI: 10.1098/rsbl.2017.0050] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys.
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Affiliation(s)
- Rachel L Jacobs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA .,Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar
| | - Tammie S MacFie
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Amanda N Spriggs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA.,Department of Anthropology, University at Albany-SUNY, Albany, NY 12222, USA
| | - Andrea L Baden
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Anthropology, Hunter College-CUNY, and The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | - Toni Lyn Morelli
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Jennifer Pastorini
- Anthropologisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mireya Mayor
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar
| | - Runhua Lei
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Ryan Culligan
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Melissa T R Hawkins
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Peter M Kappeler
- Behavioural Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen 37077, Germany
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Edward E Louis
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | | | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
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32
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Janiak MC, Chaney ME, Tosi AJ. Evolution of Acidic Mammalian Chitinase Genes (CHIA) Is Related to Body Mass and Insectivory in Primates. Mol Biol Evol 2017; 35:607-622. [PMID: 29216399 DOI: 10.1093/molbev/msx312] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insects are an important food resource for many primates, but the chitinous exoskeletons of arthropods have long been considered to be indigestible by the digestive enzymes of most mammals. However, recently mice and insectivorous bats were found to produce the enzyme acidic mammalian chitinase (AMCase) to digest insect exoskeletons. Here, we report on the gene CHIA and its paralogs, which encode AMCase, in a comparative sample of nonhuman primates. Our results show that early primates likely had three CHIA genes, suggesting that insects were an important component of the ancestral primate diet. With some exceptions, most extant primate species retain only one functional CHIA paralog. The exceptions include two colobine species, in which all CHIA genes have premature stop codons, and several New World monkey species that retain two functional genes. The most insectivorous species in our sample also have the largest number of functional CHIA genes. Tupaia chinensis and Otolemur garnettii retain three functional CHIA paralogs, whereas Tarsius syrichta has a total of five, two of which may be duplications specific to the tarsier lineage. Selection analyses indicate that CHIA genes are under more intense selection in species with higher insect consumption, as well as in smaller-bodied species (<500 g), providing molecular support for Kay's Threshold, a well-established component of primatological theory which proposes that only small primates can be primarily insectivorous. These findings suggest that primates, like mice and insectivorous bats, may use the enzyme AMCase to digest the chitin in insect exoskeletons, providing potentially significant nutritional benefits.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, NJ.,Center for Human Evolutionary Studies, Rutgers University, New Brunswick, NJ.,Department of Anthropology, New York University, New York, NY
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH.,School of Biomedical Sciences, Kent State University, Kent, OH
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH.,School of Biomedical Sciences, Kent State University, Kent, OH
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Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH. A massively parallel strategy for STR marker development, capture, and genotyping. Nucleic Acids Res 2017; 45:e142. [PMID: 28666376 PMCID: PMC5587753 DOI: 10.1093/nar/gkx574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3–99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen M Johnson
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Edward E Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
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Tung J, Barreiro LB. The contribution of admixture to primate evolution. Curr Opin Genet Dev 2017; 47:61-68. [PMID: 28923540 DOI: 10.1016/j.gde.2017.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression. Like other aspects of human biology, studies of nonhuman primates thus provide both comparative context and a living model for understanding admixture dynamics in hominins. We highlight several open questions that could be addressed in future work.
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Affiliation(s)
- Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Duke University Population Research Institute, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya.
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
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Salmona J, Heller R, Quéméré E, Chikhi L. Climate change and human colonization triggered habitat loss and fragmentation in Madagascar. Mol Ecol 2017; 26:5203-5222. [DOI: 10.1111/mec.14173] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Jordi Salmona
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
| | - Rasmus Heller
- Department of Biology; University of Copenhagen; Copenhagen N Denmark
| | - Erwan Quéméré
- CEFS; Université de Toulouse; INRA; Castanet-Tolosan France
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciênca; Oeiras Portugal
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS; Université Paul Sabatier; Toulouse France
- UMR 5174 EDB; Université de Toulouse; Toulouse France
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Kistler L, Ware R, Smith O, Collins M, Allaby RG. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res 2017; 45:6310-6320. [PMID: 28486705 PMCID: PMC5499742 DOI: 10.1093/nar/gkx361] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/15/2017] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.
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MESH Headings
- Base Composition
- Base Sequence
- DNA Fragmentation
- DNA, Ancient/analysis
- DNA, Ancient/chemistry
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Deamination
- Genome, Human
- Genome, Mitochondrial
- Humans
- Meta-Analysis as Topic
- Models, Chemical
- Paleontology/methods
- Sequence Analysis, DNA
- Thermodynamics
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Affiliation(s)
- Logan Kistler
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roselyn Ware
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Oliver Smith
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark
| | - Matthew Collins
- Section for Evolutionary Genomics, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1307 Copenhagen K, Denmark
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - Robin G. Allaby
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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Tavares WC, Seuánez HN. Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PLoS One 2017; 12:e0177403. [PMID: 28510580 PMCID: PMC5433710 DOI: 10.1371/journal.pone.0177403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/26/2017] [Indexed: 01/09/2023] Open
Abstract
Several human diseases have been associated with mutations in mitochondrial genes comprising a set of confirmed and reported mutations according to the MITOMAP database. An analysis of complete mitogenomes across 139 primate species showed that most confirmed disease-associated mutations occurred in aligned codon positions and gene regions under strong purifying selection resulting in a strong evolutionary conservation. Only two confirmed variants (7.1%), coding for the same amino acids accounting for severe human diseases, were identified without apparent pathogenicity in non-human primates, like the closely related Bornean orangutan. Conversely, reported disease-associated mutations were not especially concentrated in conserved codon positions, and a large fraction of them occurred in highly variable ones. Additionally, 88 (45.8%) of reported mutations showed similar variants in several non-human primates and some of them have been present in extinct species of the genus Homo. Considering that recurrent mutations leading to persistent variants throughout the evolutionary diversification of primates are less likely to be severely damaging to fitness, we suggest that these 88 mutations are less likely to be pathogenic. Conversely, 69 (35.9%) of reported disease-associated mutations occurred in extremely conserved aligned codon positions which makes them more likely to damage the primate mitochondrial physiology.
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Affiliation(s)
- William Corrêa Tavares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 2017; 5:e3033. [PMID: 28316883 PMCID: PMC5354071 DOI: 10.7717/peerj.3033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
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Affiliation(s)
- Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; BioArCh, Department of Archaeology, University of York, York, UK
| | - Geoff M Smith
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Jarod M Hutson
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Current affiliation: Department of Paleobiology, Smithsonian Institution, Washington, D.C., USA
| | - Lutz Kindler
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Alejandro Garcia-Moreno
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Aritza Villaluenga
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Elaine Turner
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Sabine Gaudzinski-Windheuser
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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Peichl L, Kaiser A, Rakotondraparany F, Dubielzig RR, Goodman SM, Kappeler PM. Diversity of photoreceptor arrangements in nocturnal, cathemeral and diurnal Malagasy lemurs. J Comp Neurol 2017; 527:13-37. [DOI: 10.1002/cne.24167] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Leo Peichl
- Max Planck Institute for Brain Research; Max-von-Laue-Straße 4, 60438 Frankfurt am Main Germany
- Ernst Strüngmann Institute for Neuroscience; Deutschordenstraße 46, 60528 Frankfurt am Main Germany
- Institute of Cellular and Molecular Anatomy, Dr. Senckenbergische Anatomie, Goethe University Frankfurt; Theodor-Stern-Kai 7, 60590 Frankfurt am Main Germany
| | - Alexander Kaiser
- Department Biology II; Ludwig-Maximilians University Munich; Großhaderner Straße 2-4, 82152 Martinsried-Planegg Germany
- Institute of Zoology; University of Veterinary Medicine Hannover; Bünteweg 17, 30559 Hannover Germany
| | - Felix Rakotondraparany
- Département de Zoologie et Biodiversité Animale; Université d’Antananarivo; BP 906, Antananarivo 101 Madagascar
| | - Richard R. Dubielzig
- School of Veterinary Medicine; University of Wisconsin; 2015 Linden Drive Madison Wisconsin 53706
| | - Steven M. Goodman
- The Field Museum of Natural History; 1400 South Lake Shore Drive, Chicago Illinois 60605
- Association Vahatra; BP 3972, Antananarivo 101 Madagascar
| | - Peter M. Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center; Kellnerweg 4, 37077 Göttingen Germany
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology; University Göttingen; Kellnerweg 6, 37077 Göttingen Germany
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40
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Herrera JP. Testing the adaptive radiation hypothesis for the lemurs of Madagascar. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161014. [PMID: 28280597 PMCID: PMC5319363 DOI: 10.1098/rsos.161014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 05/12/2023]
Abstract
Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.
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Affiliation(s)
- James P. Herrera
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Author for correspondence: James P. Herrera e-mail:
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Marchi D, Ruff CB, Capobianco A, Rafferty KL, Habib MB, Patel BA. The locomotion ofBabakotia radofilaiinferred from epiphyseal and diaphyseal morphology of the humerus and femur. J Morphol 2016; 277:1199-218. [DOI: 10.1002/jmor.20569] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/06/2016] [Accepted: 05/27/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Damiano Marchi
- Department of Biology; University of Pisa; Pisa 56126 Italy
- Evolutionary Studies Institute, University of the Witwatersrand; Johannesburg WITS 2050 South Africa
| | - Christopher B. Ruff
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine; Baltimore Maryland 21111
| | - Alessio Capobianco
- Department of Biology; University of Pisa; Pisa 56126 Italy
- Scuola Normale Superiore; Pisa 56126 Italy
| | - Katherine L. Rafferty
- Department of Orthodontics School of Dentistry; University of Washington; Seattle Washington 98195
| | - Michael B. Habib
- Department of Cell and Neurobiology Keck School of Medicine; University of Southern California; Los Angeles California 90033
| | - Biren A. Patel
- Evolutionary Studies Institute, University of the Witwatersrand; Johannesburg WITS 2050 South Africa
- Department of Cell and Neurobiology Keck School of Medicine; University of Southern California; Los Angeles California 90033
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42
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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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43
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The phylogenetic system of primates—character evolution in the light of a consolidated tree. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0279-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Abstract
Madagascar's lemurs display a diverse array of feeding strategies with complex relationships to seed dispersal mechanisms in Malagasy plants. Although these relationships have been explored previously on a case-by-case basis, we present here the first comprehensive analysis of lemuriform feeding, to our knowledge, and its hypothesized effects on seed dispersal and the long-term survival of Malagasy plant lineages. We used a molecular phylogenetic framework to examine the mode and tempo of diet evolution, and to quantify the associated morphological space occupied by Madagascar's lemurs, both extinct and extant. Using statistical models and morphometric analyses, we demonstrate that the extinction of large-bodied lemurs resulted in a significant reduction in functional morphological space associated with seed dispersal ability. These reductions carry potentially far-reaching consequences for Malagasy ecosystems, and we highlight large-seeded Malagasy plants that appear to be without extant animal dispersers. We also identify living lemurs that are endangered yet occupy unique and essential dispersal niches defined by our morphometric analyses.
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45
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Godfrey LR, Granatosky MC, Jungers WL. The Hands of Subfossil Lemurs. DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-3646-5_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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46
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dos Reis M, Donoghue PCJ, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era. Nat Rev Genet 2015; 17:71-80. [PMID: 26688196 DOI: 10.1038/nrg.2015.8] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.
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Affiliation(s)
- Mario dos Reis
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Malhi RS, Bader AC. ENGAGING NATIVE AMERICANS IN GENOMICS RESEARCH. AMERICAN ANTHROPOLOGIST 2015; 117:743-744. [PMID: 27799658 DOI: 10.1111/aman.12369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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48
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Godfrey LR, Crowley BE, Muldoon KM, Kelley EA, King SJ, Best AW, Berthaume MA. What did Hadropithecus eat, and why should paleoanthropologists care? Am J Primatol 2015; 78:1098-112. [PMID: 26613562 DOI: 10.1002/ajp.22506] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 11/05/2022]
Abstract
Over 40 years ago, Clifford Jolly noted different ways in which Hadropithecus stenognathus converged in its craniodental anatomy with basal hominins and with geladas. The Malagasy subfossil lemur Hadropithecus departs from its sister taxon, Archaeolemur, in that it displays comparatively large molars, reduced incisors and canines, a shortened rostrum, and thickened mandibular corpus. Its molars, however, look nothing like those of basal hominins; rather, they much more closely resemble molars of grazers such as Theropithecus. A number of tools have been used to interpret these traits, including dental microwear and texture analysis, molar internal and external morphology, and finite element analysis of crania. These tools, however, have failed to provide support for a simple dietary interpretation; whereas there is some consistency in the inferences they support, dietary inferences (e.g., that it was graminivorous, or that it specialized on hard objects) have been downright contradictory. Cranial shape may correlate poorly with diet. But a fundamental question remains unresolved: why do the various cranial and dental convergences exemplified by Hadropithecus, basal hominins, and Theropithecus exist? In this paper we review prior hypotheses regarding the diet of Hadropithecus. We then use stable carbon and nitrogen isotope data to elucidate this species' diet, summarizing earlier stable isotope analyses and presenting new data for lemurs from the central highlands of Madagascar, where Hadropithecus exhibits an isotopic signature strikingly different from that seen in other parts of the island. We offer a dietary explanation for these differences. Hadropithecus likely specialized neither on grasses nor hard objects; its staples were probably the succulent leaves of CAM plants. Nevertheless, aspects of prior hypotheses regarding the ecological significance of its morphology can be supported. Am. J. Primatol. 78:1098-1112, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts.
| | - Brooke E Crowley
- Departments of Geology and Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Kathleen M Muldoon
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona
| | - Elizabeth A Kelley
- Department of Sociology and Anthropology, Saint Louis University, St. Louis, Missouri
| | - Stephen J King
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts
| | - Andrew W Best
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts
| | - Michael A Berthaume
- Max Planck Weizmann Center for Integrative Archaeology and Anthropology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Kamilar JM, Tecot SR. Anthropogenic and Climatic Effects on the Distribution of Eulemur Species: An Ecological Niche Modeling Approach. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9875-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Yao H, Gao M, Liu K, Zhao S. Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4431-4432. [PMID: 26406276 DOI: 10.3109/19401736.2015.1089558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Verreaux's sifaka, Propithecus verreauxi, is a medium-sized lemur that inhabits in tropical dry lowland and montane forest. Here, we reported the complete mitochondrial genome sequence of this species. The mitogenome of P. verreauxi is 17 106 bp in length and composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structure about gene order and composition is identical to that of the other lemur species and related genera. The overall base composition of the heavy strand in descending order is A (32.84%), T (27.13%), C (26.95%), and G (13.08%). Most of the genes are encoded on the heavy strand except for the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes. With the exception of COX3, which terminates with an incomplete stop codon (T-), all the other PCGs initiates with a traditional ATN start codon and ends with the typical mitochondrial stop codon (TAG/TAA/AGA). The phylogenetic tree constructed using the complete mitochondrial genome sequences of P. verreauxi together with 15 other closely related species with Neighbor-Joining (NJ) method shows that P. verreauxi is closer to P. coquereli in the phylogenetic relationship.
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Affiliation(s)
- Hongmei Yao
- a Department of Gynecology , Affiliated Hospital of Jining Medical University , Jining , China
| | - Min Gao
- b Department of Clinical Laboratory , Jining NO.1 People's Hospital , Jining , China
| | - Kun Liu
- c Department of Clinical College , Jining Medical University , Jining , China , and
| | - Shaojie Zhao
- d Department of Gynecology , Wuxi Maternal and Child Health Hospital , Wuxi, 214002 , China
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