1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Poofery J, Ngamprasertwong T, Narapakdeesakul D, Arnuphapprasert A, Nugraheni YR, Thanee S, Asada M, Kaneko O, Kaewthamasorn M. Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species. Sci Rep 2023; 13:20258. [PMID: 37985797 PMCID: PMC10662395 DOI: 10.1038/s41598-023-45551-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: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
In recent phylogenetic studies, bat Polychromophilus and ungulate Plasmodium, two relatively understudied haemosporidian parasites within the Apicomplexa phylum, have often been overlooked. Instead, the focus has been primarily on haemosporidian parasites in primates, rodents, and birds. Several phylogenetic analyses of bat Polychromophilus have relied on limited datasets and short informative DNA sequences. As a result of these inherent limitations, the substantiation of their evolutionary stance has encountered a diminished degree of robust validation. This study successfully obtained complete mitochondrial genome sequences from 11 Polychromophilus parasites originating from Hipposideros gentilis and Myotis siligoensis bats for the first time. Additionally, the authors have sequenced the apicoplast caseinolytic protease C genes from Polychromophilus murinus and a potentially new Polychromophilus species. These mitochondrial genomes range in length from 5994 to 6001 bp and consist of three protein-coding genes (PCGs), seven small subunit ribosomal RNA genes (SSU rRNA), 12 large subunit ribosomal RNA genes (LSU rRNA), and seven miscellaneous RNA genes. Phylogenetic analyses using Bayesian Inference and Maximum Likelihood methods indicated robust support for the grouping of ungulate Plasmodium and bat Polychromophilus in a single clade separate from other Plasmodium spp., confirming previous reports, albeit with stronger evidence in this study. The divergence between Polychromophilus in bats and Plasmodium in ungulates occurred approximately 29.61 to 55.77 million years ago (Mya), with a node age estimated at 40.63 Mya. These findings highlight that the genus Plasmodium, which includes species found in ungulates, birds, reptiles, and other mammals, does not form a monophyletic group. By incorporating Polychromophilus in bats and Plasmodium in ungulates, this study contributes significantly to understanding the phylogenetic relationships within the Haemosporida order. It provides valuable insights into the evolutionary history and interconnections among these diverse parasites, thereby expanding knowledge in this field.
Collapse
Affiliation(s)
- Juthathip Poofery
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Duriyang Narapakdeesakul
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Veterinary Pathobiology Graduate Program, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Apinya Arnuphapprasert
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Yudhi Ratna Nugraheni
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Sleman, Indonesia
| | - Suchansa Thanee
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Masahito Asada
- Research Unit for Global Infection Control, National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Morakot Kaewthamasorn
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Donohue ME, Hert ZL, Karrick CE, Rowe AK, Wright PC, Randriamanandaza LJ, Zakamanana F, Nomenjanahary ES, Everson KM, Weisrock DW. Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat. MICROBIAL ECOLOGY 2023; 86:2149-2160. [PMID: 37133496 DOI: 10.1007/s00248-023-02233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.
Collapse
Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA.
| | - Zoe L Hert
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Patricia C Wright
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
- Centre ValBio Research Station, Ranomafana, MD, USA
| | | | | | | | - Kathryn M Everson
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
| |
Collapse
|
6
|
Alfieri F, Botton-Divet L, Wölfer J, Nyakatura JA, Amson E. A macroevolutionary common-garden experiment reveals differentially evolvable bone organization levels in slow arboreal mammals. Commun Biol 2023; 6:995. [PMID: 37770611 PMCID: PMC10539518 DOI: 10.1038/s42003-023-05371-3] [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: 02/20/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Eco-morphological convergence, i.e., similar phenotypes evolved in ecologically convergent taxa, naturally reproduces a common-garden experiment since it allows researchers to keep ecological factors constant, studying intrinsic evolutionary drivers. The latter may result in differential evolvability that, among individual anatomical parts, causes mosaic evolution. Reconstructing the evolutionary morphology of the humerus and femur of slow arboreal mammals, we addressed mosaicism at different bone anatomical spatial scales. We compared convergence strength, using it as indicator of evolvability, between bone external shape and inner structure, with the former expected to be less evolvable and less involved in convergent evolution, due to anatomical constraints. We identify several convergent inner structural traits, while external shape only loosely follows this trend, and we find confirmation for our assumption in measures of convergence magnitude. We suggest that future macroevolutionary reconstructions based on bone morphology should include structural traits to better detect ecological effects on vertebrate diversification.
Collapse
Affiliation(s)
- Fabio Alfieri
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany.
- Museum Für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany.
| | - Léo Botton-Divet
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Jan Wölfer
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - John A Nyakatura
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Eli Amson
- Paleontology Department, Staatliches Museum für Naturkunde, Rosenstein 1-3, 70191, Stuttgart, Germany
| |
Collapse
|
7
|
Yuan J, Sun G, Xiao B, Hu J, Wang L, Taogetongqimuge, Bao L, Hou Y, Song S, Jiang S, Wu Y, Pan D, Liu Y, Westbury MV, Lai X, Sheng G. Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China. BMC Ecol Evol 2023; 23:56. [PMID: 37752413 PMCID: PMC10521388 DOI: 10.1186/s12862-023-02168-0] [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: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Woolly rhinoceros (Coelodonta antiquitatis) is a typical indicator of cold-stage climate that was widely distributed in Northern Hemisphere during the Middle-Late Pleistocene. Although a plethora of fossils have been excavated from Northern China, their phylogenetic status, intraspecific diversity and phylogeographical structure are still vague. RESULTS In the present study, we generated four mitogenomes from Late Pleistocene woolly rhinoceros in Northern China and compared them with published data. Bayesian and network analyses indicate that the analyzed individuals contain at least four maternal haplogroups, and Chinese samples fall in three of them. One of our samples belongs to a previously unidentified early diverging clade (haplogroup D), which separated from other woolly rhinoceros around 0.57 Ma (95% CI: 0.76-0.41 Ma). The timing of this clade's origin coincides with the first occurrence of woolly rhinoceros, which are thought to have evolved in Europe. Our other three samples cluster in haplogroup C, previously only identified from one specimen from Wrangel Island (ND030) and initially considered to be an isolated clade. Herein, our findings suggest that ND030 is likely descended from a northward dispersal of the individuals carrying haplogroup C from Northern China. Additionally, Chinese woolly rhinoceros specimens exhibit higher nucleotide diversity than those from Siberia. CONCLUSION Our findings highlight Northern China as a possible refugium and a key evolution center of the Pleistocene woolly rhinoceros.
Collapse
Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China.
| | - Guojiang Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Linying Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
- College of Earth and Environmental Science, Lanzhou University, Lanzhou, 730099, China
| | | | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos, 017010, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shiwen Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
| | - Shan Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Yong Wu
- The Third Geological and Mineral Exploration Institute of Gansu Bureau of Geology and Mineral Resources, Lanzhou, 730050, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua, 151600, China
| | - Yang Liu
- School of Sociology & Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China.
| |
Collapse
|
8
|
Suárez-Menéndez M, Bérubé M, Furni F, Rivera-León VE, Heide-Jørgensen MP, Larsen F, Sears R, Ramp C, Eriksson BK, Etienne RS, Robbins J, Palsbøll PJ. Wild pedigrees inform mutation rates and historic abundance in baleen whales. Science 2023; 381:990-995. [PMID: 37651509 DOI: 10.1126/science.adf2160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.
Collapse
Affiliation(s)
- Marcos Suárez-Menéndez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
| | - Fabrício Furni
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Vania E Rivera-León
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Finn Larsen
- National Institute of Aquatic Resources, Kongens Lyngby, Denmark
| | - Richard Sears
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
| | - Christian Ramp
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
- Scottish Oceans Institute, University of St. Andrews, St. Andrews, UK
| | - Britas Klemens Eriksson
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Per J Palsbøll
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
| |
Collapse
|
9
|
van Elst T, Schüßler D, Rakotondravony R, Rovanirina VST, Veillet A, Hohenlohe PA, Ratsimbazafy JH, Rasoloarison RM, Rasoloharijaona S, Randrianambinina B, Ramilison ML, Yoder AD, Louis EE, Radespiel U. Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests. Ecol Evol 2023; 13:e10254. [PMID: 37408627 PMCID: PMC10318617 DOI: 10.1002/ece3.10254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Madagascar exhibits exceptionally high levels of biodiversity and endemism. Models to explain the diversification and distribution of species in Madagascar stress the importance of historical variability in climate conditions which may have led to the formation of geographic barriers by changing water and habitat availability. The relative importance of these models for the diversification of the various forest-adapted taxa of Madagascar has yet to be understood. Here, we reconstructed the phylogeographic history of Gerp's mouse lemur (Microcebus gerpi) to identify relevant mechanisms and drivers of diversification in Madagascar's humid rainforests. We used restriction site associated DNA (RAD) markers and applied population genomic and coalescent-based techniques to estimate genetic diversity, population structure, gene flow and divergence times among M. gerpi populations and its two sister species M. jollyae and M. marohita. Genomic results were complemented with ecological niche models to better understand the relative barrier function of rivers and altitude. We show that M. gerpi diversified during the late Pleistocene. The inferred ecological niche, patterns of gene flow and genetic differentiation in M. gerpi suggest that the potential for rivers to act as biogeographic barriers depended on both size and elevation of headwaters. Populations on opposite sides of the largest river in the area with headwaters that extend far into the highlands show particularly high genetic differentiation, whereas rivers with lower elevation headwaters have weaker barrier functions, indicated by higher migration rates and admixture. We conclude that M. gerpi likely diversified through repeated cycles of dispersal punctuated by isolation to refugia as a result of paleoclimatic fluctuations during the Pleistocene. We argue that this diversification scenario serves as a model of diversification for other rainforest taxa that are similarly limited by geographic factors. In addition, we highlight conservation implications for this critically endangered species, which faces extreme habitat loss and fragmentation.
Collapse
Affiliation(s)
- Tobias van Elst
- Institute of ZoologyUniversity of Veterinary Medicine Hannover, FoundationHannoverGermany
| | - Dominik Schüßler
- Research Group Vegetation Ecology and Nature Conservation, Institute of Biology and ChemistryUniversity of HildesheimHildesheimGermany
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Valisoa S. T. Rovanirina
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | | | | | - Solofonirina Rasoloharijaona
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Blanchard Randrianambinina
- Ecole Doctorale Ecosystèmes Naturels (EDEN)University of MahajangaMahajangaMadagascar
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
| | - Miarisoa L. Ramilison
- Faculté des Sciences, de Technologies et de l'EnvironnementUniversity of MahajangaMahajangaMadagascar
- Department of Primate Behavior and EcologyCentral Washington UniversityEllensburgWashingtonUSA
| | - Anne D. Yoder
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Edward E. Louis
- Grewcock Center for Conservation and ResearchOmaha's Henry Doorly Zoo and AquariumOmahaNebraskaUSA
| | - Ute Radespiel
- Institute of ZoologyUniversity of Veterinary Medicine Hannover, FoundationHannoverGermany
| |
Collapse
|
10
|
Springer A, Durden LA, Kiene F, Klein A, Rakotondravony R, Ehlers J, Greiman SE, Blanco MB, Zohdy S, Kessler SE, Strube C, Radespiel U. Molecular phylogenetics of the sucking louse genus Lemurpediculus (Insecta: Phthiraptera), ectoparasites of lemurs, with descriptions of three new species. Int J Parasitol Parasites Wildl 2023; 20:138-152. [PMID: 36845223 PMCID: PMC9945782 DOI: 10.1016/j.ijppaw.2023.02.002] [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: 11/11/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Sucking lice live in intimate association with their hosts and often display a high degree of host specificity. The present study investigated sucking lice of the genus Lemurpediculus from six mouse lemur (Microcebus) and two dwarf lemur (Cheirogaleus) species endemic to the island of Madagascar, considered a biodiversity hotspot. Louse phylogenetic trees were created based on cytochrome C oxidase subunit I (COI), elongation factor 1α (EF1α) and internal transcribed spacer 1 (ITS1) sequences. While clustering according to host species was generally observed for COI and ITS1, suggesting high host specificity of the examined lice, EF1α sequences alone did not distinguish between lice of different Microcebus species, possibly due to rather recent divergence. As bootstrap support for basal tree structure was rather low, further data are necessary to resolve the evolutionary history of louse-mouse lemur associations. Three new species of sucking lice are described: Lemurpediculus zimmermanni sp. Nov. From Microcebus ravelobensis, Lemurpediculus gerpi sp.nov. from Microcebus gerpi, and Lemurpediculus tsimanampesotsae sp. nov. from Microcebus griseorufus. These new species are compared with all known congeneric species and identifying features are illustrated for all known species of Lemurpediculus.
Collapse
Affiliation(s)
- Andrea Springer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hanover, Germany
| | - Lance A. Durden
- Department of Biology, Georgia Southern University, 4324 Old Register Road, Statesboro, GA, 30458, USA
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany,Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, 30173, Hannover, Germany
| | - Annette Klein
- Institute of Zoology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany
| | - Romule Rakotondravony
- École Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, Mahajanga 401, Madagascar,Faculté des Sciences, de Technologies et de l’Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652. Mahajanga 401, Madagascar
| | - Julian Ehlers
- Animal Ecology and Conservation, Institute of Cell and Systems Biology of Animals, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Stephen E. Greiman
- Department of Biology, Georgia Southern University, 4324 Old Register Road, Statesboro, GA, 30458, USA
| | - Marina B. Blanco
- Duke Lemur Center, Durham, NC, 27705, USA,Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Sarah Zohdy
- School of Forestry and Wildlife Sciences, 602 Duncan Drive, Auburn, AL, 36849, USA
| | - Sharon E. Kessler
- Department of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hanover, Germany,Corresponding author.
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559, Hannover, Germany,Corresponding author.
| |
Collapse
|
11
|
Towle I, Constantino PJ, Borths MR, Loch C. Tooth chipping patterns in Archaeolemur provide insight into diet and behavior. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:401-408. [PMID: 36790760 PMCID: PMC10107942 DOI: 10.1002/ajpa.24674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/20/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Archaeolemur is a recently extinct genus of lemur that is often compared to some Cercopithecidae, especially baboons. This is due in part to their derived dentition, with large anterior teeth and reduced bilophodont molars. Research involving comparative morphology, analysis of coprolites, isotopes, and enamel structure, have suggested Archaeolemur had an omnivorous diet involving mechanically challenging items. Yet, microwear analysis of posterior teeth does not necessarily support this conclusion. MATERIALS AND METHODS In this macroscopic study, dental chipping was recorded on permanent teeth of Archaeolemur from different localities (53 individuals; 447 permanent teeth; including both A. edwardsi and A. majori specimens). This study aimed to compare chipping patterns across the dentition of Archaeolemur with chipping in other primates. RESULTS The results show enamel chipping was prevalent on the anterior teeth of Archaeolemur (38.9% of anterior teeth showed at least one fracture) yet rare in posterior teeth (9%). There was a decrease in chipping frequency across the dentition, moving distally from incisors (50%; 20/40), through caniniform teeth (30%; 15/50), premolars (9.5%; 16/169), and molars (8.5%; 16/188). DISCUSSION The results support previous research suggesting Archaeolemur had a varied omnivorous diet in which the anterior dentition was used for extensive food processing. This likely included mechanically challenging items such as tough/hard large fruits, small vertebrates, and crustaceans. Such a high rate of chipping in the anterior dentition is uncommon in other primates, with exception of hominins.
Collapse
Affiliation(s)
- Ian Towle
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Paul J Constantino
- Department of Biology, Saint Michael's College, Colchester, Vermont, USA
| | - Matthew R Borths
- Duke Lemur Center Museum of Natural History, Duke University, Durham, North Carolina, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| |
Collapse
|
12
|
The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nat Commun 2023; 14:14. [PMID: 36627274 PMCID: PMC9832013 DOI: 10.1038/s41467-022-35215-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 01/12/2023] Open
Abstract
Many of Madagascar's unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar's mammalian biodiversity under these rates, the "evolutionary return time" (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.
Collapse
|
13
|
Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
Collapse
Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| |
Collapse
|
14
|
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.
Collapse
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
| | | |
Collapse
|
15
|
Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
Collapse
Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| |
Collapse
|
16
|
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.
Collapse
|
17
|
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.
Collapse
|
18
|
López-Aguirre C, Lang MM, Silcox MT. Diet drove brain and dental morphological coevolution in strepsirrhine primates. PLoS One 2022; 17:e0269041. [PMID: 35666739 PMCID: PMC9170099 DOI: 10.1371/journal.pone.0269041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
The evolution of the remarkably complex primate brain has been a topic of great interest for decades. Multiple factors have been proposed to explain the comparatively larger primate brain (relative to body mass), with recent studies indicating diet has the greatest explanatory power. Dietary specialisations also correlate with dental adaptations, providing a potential evolutionary link between brain and dental morphological evolution. However, unambiguous evidence of association between brain and dental phenotypes in primates remains elusive. Here we investigate the effect of diet on variation in primate brain and dental morphology and test whether the two anatomical systems coevolved. We focused on the primate suborder Strepsirrhini, a living primate group that occupies a very wide range of dietary niches. By making use of both geometric morphometrics and dental topographic analysis, we extend the study of brain-dental ecomorphological evolution beyond measures of size. After controlling for allometry and evolutionary relatedness, differences in brain and dental morphology were found between dietary groups, and brain and dental morphologies were found to covary. Historical trajectories of morphological diversification revealed a strong integration in the rates of brain and dental evolution and similarities in their modes of evolution. Combined, our results reveal an interplay between brain and dental ecomorphological adaptations throughout strepsirrhine evolution that can be linked to diet.
Collapse
Affiliation(s)
- Camilo López-Aguirre
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
- * E-mail:
| | - Madlen M. Lang
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mary T. Silcox
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Donohue ME, Rowe AK, Kowalewski E, Hert ZL, Karrick CE, Randriamanandaza LJ, Zakamanana F, Nomenjanahary S, Andriamalala RY, Everson KM, Law AD, Moe L, Wright PC, Weisrock DW. Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME COMMUNICATIONS 2022; 2:33. [PMID: 37938265 PMCID: PMC9723590 DOI: 10.1038/s43705-022-00115-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 04/27/2023]
Abstract
Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.
Collapse
Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, NY, USA
| | - Eric Kowalewski
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Zoe L Hert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | | | - Stela Nomenjanahary
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | - Rostant Y Andriamalala
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | | | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Luke Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Madagascar
- Department of Anthropology, Stony Brook University, Stony Brook, New York, NY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
21
|
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.
Collapse
|
22
|
Ho CLA, Fichtel C, Huber D. The gray mouse lemur (Microcebus murinus) as a model for early primate brain evolution. Curr Opin Neurobiol 2021; 71:92-99. [PMID: 34768148 DOI: 10.1016/j.conb.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022]
Abstract
The gray mouse lemur (Microcebus murinus), one of the world's smallest primates, is thought to share a similar ecological niche and many anatomical traits with early euprimates. As a result, it has been considered a suitable model system for early primate physiology and behavior. Moreover, recent studies have demonstrated that mouse lemurs have comparable cognitive abilities and cortical functional organization as haplorhines. Finally, the small brain size of mouse lemurs provides us with actual lower limits for miniaturization of functional brain circuits within the primate clade. Considering its phylogenetic position and early primate-like traits, the mouse lemurs are a perfect model species to study the early evolution of primate brains.
Collapse
Affiliation(s)
- Chun Lum Andy Ho
- University of Geneva, Department of Basic Neurosciences, Rue Michel Servet 1, 1206 Geneva, Switzerland
| | - Claudia Fichtel
- Verhaltensökologie und Soziobiologie, Deutsches Primatenzentrum, Kellnerweg 4, 37077 Göttingen, Germany; Leibniz Science Campus 'Primate Cognition', 37077 Göttingen, Germany
| | - Daniel Huber
- University of Geneva, Department of Basic Neurosciences, Rue Michel Servet 1, 1206 Geneva, Switzerland.
| |
Collapse
|
23
|
Toda Y, Hayakawa T, Itoigawa A, Kurihara Y, Nakagita T, Hayashi M, Ashino R, Melin AD, Ishimaru Y, Kawamura S, Imai H, Misaka T. Evolution of the primate glutamate taste sensor from a nucleotide sensor. Curr Biol 2021; 31:4641-4649.e5. [PMID: 34450087 DOI: 10.1016/j.cub.2021.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
Taste perception plays an essential role in food selection. Umami (savory) tastes are sensed by a taste receptor complex, T1R1/T1R3, that detects proteinogenic amino acids.1 High sensitivity to l-glutamate (l-Glu) is a characteristic of human T1R1/T1R3, but the T1R1/T1R3 of other vertebrates does not consistently show this l-Glu response.1,2 Here, we demonstrate that the l-Glu sensitivity of T1R1/T1R3 is a derived state that has evolved repeatedly in large primates that rely on leaves as protein sources, after their divergence from insectivorous ancestors. Receptor expression experiments show that common amino acid substitutions at ligand binding sites that render T1R1/T1R3 sensitive to l-Glu occur independently at least three times in primate evolution. Meanwhile T1R1/T1R3 senses 5'-ribonucleotides as opposed to l-Glu in several mammalian species, including insectivorous primates. Our chemical analysis reveal that l-Glu is one of the major free amino acids in primate diets and that insects, but not leaves, contain large amounts of free 5'-ribonucleotides. Altering the ligand-binding preference of T1R1/T1R3 from 5'-ribonucleotides to l-Glu might promote leaf consumption, overcoming bitter and aversive tastes. Altogether, our results provide insight into the foraging ecology of a diverse mammalian radiation and help reveal how evolution of sensory genes facilitates invasion of new ecological niches.
Collapse
Affiliation(s)
- Yasuka Toda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan; Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Akihiro Itoigawa
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan; Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Yosuke Kurihara
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Center for Education and Research in Field Sciences, Faculty of Agriculture, Shizuoka University, Hamamatsu, Shizuoka 431-3532, Japan
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masahiro Hayashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Ryuichi Ashino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta T2N 1N4, Canada; Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan.
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
| |
Collapse
|
24
|
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.
Collapse
|
25
|
Campbell CR, Tiley GP, Poelstra JW, Hunnicutt KE, Larsen PA, Lee HJ, Thorne JL, Dos Reis M, Yoder AD. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity (Edinb) 2021; 127:233-244. [PMID: 34272504 PMCID: PMC8322134 DOI: 10.1038/s41437-021-00446-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be among the highest calculated for a mammal at 1.52 × 10-8 (95% credible interval: 1.28 × 10-8-1.78 × 10-8) mutations/site/generation. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false-negative and false-positive rate for our data and show that any point estimate of a de novo mutation rate should be considered with a large degree of uncertainty. For validation, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which de novo mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution-rate analyses for all species compared.
Collapse
Affiliation(s)
- C Ryan Campbell
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | - Kelsie E Hunnicutt
- Department of Biology, Duke University, Durham, NC, USA
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Peter A Larsen
- Department of Biology, Duke University, Durham, NC, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Hui-Jie Lee
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Quintero-Galvis JF, Saenz-Agudelo P, Celis-Diez JL, Amico GC, Vazquez S, Shafer ABA, Nespolo RF. The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus. Mol Phylogenet Evol 2021; 163:107234. [PMID: 34146676 DOI: 10.1016/j.ympev.2021.107234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 01/16/2023]
Abstract
The current distribution of the flora and fauna of southern South America is the result of drastic geological events that occurred during the last 20 million years, including marine transgressions, glaciations and active vulcanism. All these have been associated with fragmentation, isolation and subsequent expansion of the biota, south of 35°S, such as the temperate rainforest. This forest is mostly dominated by Nothofagus trees and is the habitat of the relict marsupial monito del monte, genus Dromiciops, sole survivor of the order Microbiotheria. Preliminary analyses using mtDNA proposed the existence of three main Dromiciops lineages, distributed latitudinally, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocene) biogeographic history for the genus. We performed phylogenetic reconstructions using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens from 31 sites across Chile and Argentina. Our phylogenetic analysis resolved three main clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which should be considered a distinct species (D. bozinovici, sensu D'Elía et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about ~13 million years ago. Divergence time estimates for the southern clades (39.6°S to 42.0°S) ranged from 9.57 to 6.5 Mya. A strong genetic structure was also detected within and between clades. Demographic analyses suggest population size stability for the northern clade (D. bozinovici), and recent demographic expansions for the central and southern clades. All together, our results suggest that the diversification of Dromiciops were initiated by the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of Los Andes between 37 and 48°S. The MMT resulted from an increase in global sea levels at the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat of Dromiciops.
Collapse
Affiliation(s)
- Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan L Celis-Diez
- Pontificia Universidad Católica de Valparaíso Escuela de Agronomía Quillota, Chile
| | - Guillermo C Amico
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Soledad Vazquez
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Aaron B A Shafer
- Department of Forensic Science & Environmental Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
| |
Collapse
|
28
|
Sefczek TM, McGraw WS, Faralahy DM, Manampisoa GM, Louis EE. Locomotion of an adult female and juvenile male aye-aye (Daubentonia madagascariensis) in Torotorofotsy, Madagascar. Am J Primatol 2021; 83:e23267. [PMID: 33956356 DOI: 10.1002/ajp.23267] [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: 08/31/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 11/09/2022]
Abstract
Aye-ayes (Daubentonia madagascariensis) locate and acquire invertebrates from within woody substrates at all levels of the rainforest; yet how their locomotion helps them accommodate this diet has not been explored in detail. We studied the locomotor behavior of an adult female (N = 1,085) and juvenile male (N = 708) aye-aye in the undisturbed forest of Torotorofotsy, Madagascar from May to December 2017. We used bout sampling to record locomotion during foraging and travel of the two radio-collared individuals. We used χ 2 tests to compare overall locomotion, travel, and foraging, as well as strata and support use. We performed a correspondence analysis to examine relationships between individual behaviors, strata, and support types. Leaping accounted for 47.9% and 50.1% of all locomotor activity in the adult female and juvenile male, respectively. Leaping was the most common behavior during travel in both individuals (59.2% and 53.9%, respectively), whereas head-first descent was most frequent during foraging (35.0% and 48.0%, respectively). For all three locomotor categories, the main canopy (40.3%-79.6%) was used most frequently and trunks were the most frequently used support type (50.7%-60.0%). There is a strong association between strata and support use overall and during travel. Quadrupedal walking was significantly associated with the main canopy, as was head-first descent with the low canopy. Our analysis demonstrates that aye-ayes use a variety of locomotor behaviors to forage for invertebrates. Aye-ayes' ability to repurpose their positional repertoire to acquire other resources in degraded forests should not obscure the importance of invertebrates to this species.
Collapse
Affiliation(s)
- Timothy M Sefczek
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA.,Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | - W Scott McGraw
- Department of Anthropology, The Ohio State University, Columbus, Ohio, USA
| | | | | | - Edward E Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA.,Madagascar Biodiversity Partnership, Antananarivo, Madagascar
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Linguistic laws of brevity: conformity in Indri indri. Anim Cogn 2021; 24:897-906. [PMID: 33683508 DOI: 10.1007/s10071-021-01495-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/23/2021] [Accepted: 02/19/2021] [Indexed: 02/03/2023]
Abstract
Vocal and gestural sequences of several primates have been found to conform to two general principles of information compression: the compensation between the duration of a construct and that of its components (Menzerath-Altmann law) and an inverse relationship between signal duration and its occurrence (Zipf's law of abbreviation). Even though Zipf's law of brevity has been proposed as a universal in animal communication, evidence on non-human primate vocal behavior conformity to linguistic laws is still debated, and information on strepsirrhine primates is lacking. We analyzed the vocal behavior of the unique singing lemur species (Indri indri) to assess whether the song of the species shows evidence for compression. As roars have a chaotic structure that impedes the recognition of each individual utterance, and long notes are usually given by males, we focused on the core part of the song (i.e., the descending phrases, composed of two-six units). Our results indicate that indris' songs conform to Zipf's and Menzerath-Altmann linguistic laws. Indeed, shorter phrases are more likely to be included in the song, and units' duration decrease at the increase of the size of the phrases. We also found that, despite a sexual dimorphism in the duration of both units and phrases, these laws characterize sequences of both males and females. Overall, we provide the first evidence for a trade-off between signal duration and occurrence in the vocal behavior of a strepsirrhine species, suggesting that selective pressures for vocal compression are more ancestral than previously assumed within primates.
Collapse
|
31
|
Randimbiharinirina RD, Richter T, Raharivololona BM, Ratsimbazafy JH, Schüßler D. To tell a different story: Unexpected diversity in local attitudes towards Endangered Aye‐ayes
Daubentonia madagascariensis
offers new opportunities for conservation. PEOPLE AND NATURE 2021. [DOI: 10.1002/pan3.10192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Roger Doménico Randimbiharinirina
- Mention Anthropobiologie et Développement Durable de la Faculté des Sciences University of Antananarivo Antananarivo Madagascar
- Groupe d'Etude et de Recherche sur les Primates de Madagascar (GERP) Antananarivo Madagascar
| | - Torsten Richter
- Research Group Plant Ecology and Nature Conservation University of Hildesheim Hildesheim Germany
| | - Brigitte M. Raharivololona
- Mention Anthropobiologie et Développement Durable de la Faculté des Sciences University of Antananarivo Antananarivo Madagascar
| | - Jonah H. Ratsimbazafy
- Groupe d'Etude et de Recherche sur les Primates de Madagascar (GERP) Antananarivo Madagascar
| | - Dominik Schüßler
- Research Group Plant Ecology and Nature Conservation University of Hildesheim Hildesheim Germany
| |
Collapse
|
32
|
Endogenization of a Prosimian Retrovirus during Lemur Evolution. Viruses 2021; 13:v13030383. [PMID: 33673677 PMCID: PMC7997422 DOI: 10.3390/v13030383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 01/08/2023] Open
Abstract
Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel's sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4.56 MYA (± 2.4 MYA), placing it after the divergence of Propithecus species. These results indicate that PSRV1 is an important milestone of lemur evolution during the radiation of the Propithecus genus. These findings may have implications for both human and animal health in that the acquisition of a gamma-type env gene within an endogenized betaretrovirus could facilitate a cross-species jump between vertebrate class hosts.
Collapse
|
33
|
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: 48] [Impact Index Per Article: 12.0] [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.
Collapse
|
34
|
|
35
|
Spasojevic T, Broad GR, Sääksjärvi IE, Schwarz M, Ito M, Korenko S, Klopfstein S. Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae). Syst Biol 2020; 70:322-339. [PMID: 33057674 PMCID: PMC7875445 DOI: 10.1093/sysbio/syaa079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/16/2023] Open
Abstract
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: “bare-branch attraction,” namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.]
Collapse
Affiliation(s)
- Tamara Spasojevic
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland.,Department of Entomology, National Museum of Natural History, Washington, DC 20560, USA
| | - Gavin R Broad
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | | | | | - Masato Ito
- Graduate School of Agricultural Science, Department of Agrobioscience, Kobe University, 657-8501 Japan
| | - Stanislav Korenko
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Suchdol, Czech Republic
| | - Seraina Klopfstein
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland.,Abteilung für Biowissenschaften, Naturhistorisches Museum Basel, 4051 Basel, Switzerland
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Koch NM, Parry LA. Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. Syst Biol 2020; 69:1052-1067. [DOI: 10.1093/sysbio/syaa023] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses. [phylogeny, morphology, fossils, parsimony, Bayesian inference.]
Collapse
Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
| | - Luke A Parry
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
| |
Collapse
|
39
|
Knigge RP, Vinyard CJ, McNulty KP. Mandibular symphyseal fusion in fossil primates: Insights from correlated patterns of jaw shape and masticatory function in living primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:322-336. [PMID: 32167167 DOI: 10.1002/ajpa.24048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/27/2020] [Accepted: 02/24/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Variation in primate masticatory form and function has been extensively researched through both morphological and experimental studies. As a result, symphyseal fusion in different primate clades has been linked to either the recruitment of vertically directed balancing-side muscle force, the timing and recruitment of transversely directed forces, or both. This study investigates the relationship between jaw muscle activity patterns and morphology in extant primates to make inferences about masticatory function in extinct primates, with implications for understanding the evolution of symphyseal fusion. MATERIALS AND METHODS Three-dimensional mandibular landmark data were collected for 31 extant primates and nine fossil anthropoids and subfossil lemur species. Published electromyography (EMG) data were available for nine of the extant primate species. Partial least squares analysis and phylogenetic partial least squares analysis were used to identify relationships between EMG and jaw shape data and evaluate variation in jaw morphology. RESULTS Primates with partial and complete symphyseal fusion exhibit shape-function patterns associated with the wishboning motor pattern and loading regime, in contrast to shape-function patterns of primates with unfused jaws. All fossil primates examined (except Apidium) exhibit jaw morphologies suggestive of the wishboning motor pattern demonstrated in living anthropoids and indriids. DISCUSSION Partial fusion in Catopithecus, similar to indriids and some subfossil lemurs, may be sufficient to resist, or transfer, some amounts of transversely directed balancing-side muscle force at the symphysis, representing a transition to greater reliance on transverse jaw movement during mastication. Furthermore, possible functional convergences in physiological patterns during chewing (i.e., Archaeolemur) are identified.
Collapse
Affiliation(s)
- Ryan P Knigge
- Evolutionary Anthropology Lab, Department of Anthropology, University of Minnesota, Minneapolis, Minnesota.,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri.,Department of Orthopaedic Surgery, University of Missouri, Columbia, Missouri
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio
| | - Kieran P McNulty
- Evolutionary Anthropology Lab, Department of Anthropology, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
40
|
Batist CH, Mayhew JA. Lateralization in seven lemur species when presented with a novel cognitive task. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:270-279. [PMID: 32129499 DOI: 10.1002/ajpa.24037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Asymmetrical behavior patterns are observed in many animal species, but the potential adaptive significance of lateralization and the evolutionary forces driving it remain unclear. Most laterality studies have focused on a single species, which makes interspecies comparisons difficult. The aim of this study was to examine differences in the strength and direction of lateralization in multiple lemur species when engaged in a standardized, novel cognitive task. MATERIALS AND METHODS We assessed laterality in seven lemur species at the Duke Lemur Center when using a novel puzzle-box. We recorded which hand opened the apparatus door and which hand picked up the food reward. We also recorded whether the mouth was used for either action instead of the hands. We then calculated handedness indices (HI), z-scores, and mouth-use rates. RESULTS Overall, 62% of individuals were more lateralized than chance. However, within-genera, there were relatively equal numbers of individuals with a left- or right-hand bias, which resulted in ambipreference at the genus level. The hand a lemur used on its first success in the task predicted its overall HI value, and the strength of lateralization increased as the number of successes increased. Varecia had significantly higher mouth-use rates than all other genera. DISCUSSION We found evidence of an individual learning trajectory in which the hand used on a lemur's first success was canalized as the preferred (and lateralized) hand, in support of the "cognitive simplicity" hypothesis. Individual variability in hand preference was high, which is consistent with previous research. Between-genera differences in mouth use appear to reflect species-specific feeding postures and differences in manual dexterity.
Collapse
Affiliation(s)
- Carly H Batist
- Primate Behavior and Ecology Program, Central Washington University, Ellensburg, Washington, USA
| | - Jessica A Mayhew
- Primate Behavior and Ecology Program, Central Washington University, Ellensburg, Washington, USA.,Department of Anthropology and Museum Studies, Central Washington University, Ellensburg, Washington, USA
| |
Collapse
|
41
|
Luo A, Duchêne DA, Zhang C, Zhu CD, Ho SYW. A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process. Syst Biol 2020; 69:325-344. [PMID: 31132125 PMCID: PMC7175741 DOI: 10.1093/sysbio/syz038] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022] Open
Abstract
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
Collapse
Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
42
|
Campera M, Santini L, Balestri M, Nekaris K, Donati G. Elevation gradients of lemur abundance emphasise the importance of Madagascar’s lowland rainforest for the conservation of endemic taxa. Mamm Rev 2019. [DOI: 10.1111/mam.12172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Marco Campera
- Nocturnal Primate Research Group Department of Social Sciences Oxford Brookes University Gipsy Lane OxfordOX3 0BPUnited Kingdom
| | - Luca Santini
- Department of Environmental Science Institute for Water and Wetland Research Radboud University Heyendaalseweg Nijmegen6525 HPThe Netherlands
| | - Michela Balestri
- Nocturnal Primate Research Group Department of Social Sciences Oxford Brookes University Gipsy Lane OxfordOX3 0BPUnited Kingdom
| | - K.A.I. Nekaris
- Nocturnal Primate Research Group Department of Social Sciences Oxford Brookes University Gipsy Lane OxfordOX3 0BPUnited Kingdom
| | - Giuseppe Donati
- Nocturnal Primate Research Group Department of Social Sciences Oxford Brookes University Gipsy Lane OxfordOX3 0BPUnited Kingdom
| |
Collapse
|
43
|
Greene LK, Clayton JB, Rothman RS, Semel BP, Semel MA, Gillespie TR, Wright PC, Drea CM. Local habitat, not phylogenetic relatedness, predicts gut microbiota better within folivorous than frugivorous lemur lineages. Biol Lett 2019; 15:20190028. [PMID: 31185820 DOI: 10.1098/rsbl.2019.0028] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Both host phylogenetic placement and feeding strategy influence the structure of the gut microbiome (GMB); however, parsing their relative contributions presents a challenge. To meet this challenge, we compared GMB structure in two genera of lemurs characterized by different dietary specializations, the frugivorous brown lemurs ( Eulemur spp.) and the folivorous sifakas ( Propithecus spp.). These genera sympatrically occupy similar habitats (dry forests and rainforests) and diverged over similar evolutionary timescales. We collected fresh faeces from 12 species (six per host genus), at seven sites across Madagascar, and sequenced the 16S rRNA gene to determine GMB membership, diversity and variability. The lemurs' GMBs clustered predominantly by host genus; nevertheless, within genera, host relatedness did not predict GMB distance between species. The GMBs of brown lemurs had greater evenness and diversity, but were more homogeneous across species, whereas the GMBs of sifakas were differentiated between habitats. Thus, over relatively shallow timescales, environmental factors can override the influence of host phylogenetic placement on GMB phylogenetic composition. Moreover, feeding strategy can underlie the relative strength of host-microbiome coadaptation, with Madagascar's folivores perhaps requiring locally adapted GMBs to facilitate their highly specialized diets.
Collapse
Affiliation(s)
- Lydia K Greene
- 1 Program in Ecology, Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,2 Primate Microbiome Project , Minneapolis, MN 55455 , USA
| | - Jonathan B Clayton
- 2 Primate Microbiome Project , Minneapolis, MN 55455 , USA.,3 Department of Computer Science and Engineering, University of Minnesota , Minneapolis, MN 55455 , USA
| | - Ryan S Rothman
- 4 Department of Life Sciences, Imperial College London , Silwood Park Campus, Ascot, Berks , SW7 2AZ, UK
| | - Brandon P Semel
- 5 Department of Fish and Wildlife Conservation, Virginia Tech , Blacksburg, VA 24061 , USA
| | - Meredith A Semel
- 6 Department of Biological Sciences, Virginia Tech , Blacksburg, VA 24061 , USA
| | - Thomas R Gillespie
- 2 Primate Microbiome Project , Minneapolis, MN 55455 , USA.,7 Department of Environmental Sciences, Emory University , Atlanta, GA 30322 , USA
| | - Patricia C Wright
- 8 Department of Anthropology, Stony Brook University , Stony Brook, NY 11794 , USA
| | - Christine M Drea
- 1 Program in Ecology, Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA
| |
Collapse
|
44
|
Bernardi M, Couette S, Chateau Smith C, Montuire S. Middle ear pneumatization in nonhuman primates: A comparative analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:540-556. [DOI: 10.1002/ajpa.23848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 12/03/2018] [Accepted: 04/16/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Margot Bernardi
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
| | - Sébastien Couette
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
| | | | - Sophie Montuire
- EPHEPSL Research University Paris Paris France
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐Comté Dijon France
| |
Collapse
|
45
|
Greene LK, Bornbusch SL, McKenney EA, Harris RL, Gorvetzian SR, Yoder AD, Drea CM. The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs. Am J Primatol 2019; 81:e22974. [PMID: 30932230 DOI: 10.1002/ajp.22974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022]
Abstract
Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host-microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage-specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent-gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host-microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis-driven research.
Collapse
Affiliation(s)
- Lydia K Greene
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Sally L Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Rachel L Harris
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Sarah R Gorvetzian
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, North Carolina
| | - Christine M Drea
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Department of Biology, Duke University, Durham, North Carolina
| |
Collapse
|
46
|
Kappeler PM, Nunn CL, Vining AQ, Goodman SM. Evolutionary dynamics of sexual size dimorphism in non-volant mammals following their independent colonization of Madagascar. Sci Rep 2019; 9:1454. [PMID: 30723219 PMCID: PMC6363729 DOI: 10.1038/s41598-018-36246-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/15/2018] [Indexed: 01/16/2023] Open
Abstract
As predicted by sexual selection theory, males are larger than females in most polygynous mammals, but recent studies found that ecology and life history traits also affect sexual size dimorphism (SSD) through evolutionary changes in either male size, female size, or both. The primates of Madagascar (Lemuriformes) represent the largest group of mammals without male-biased SSD. The eco-evo-devo hypothesis posited that adaptations to unusual climatic unpredictability on Madagascar have ultimately reduced SSD in lemurs after dispersing to Madagascar, but data have not been available for comparative tests of the corresponding predictions that SSD is also absent in other terrestrial Malagasy mammals and that patterns of SSD changed following the colonization of Madagascar. We used phylogenetic methods and new body mass data to test these predictions among the four endemic radiations of Malagasy primates, carnivorans, tenrecs, and rodents. In support of our prediction, we found that male-biased SSD is generally absent among all Malagasy mammals. Phylogenetic comparative analyses further indicated that after their independent colonization of Madagascar, SSD decreased in primates and tenrecs, but not in the other lineages or when analyzed across all species. We discuss several mechanisms that may have generated these patterns and conclude that neither the eco-evo-devo hypothesis, founder effects, the island rule nor sexual selection theory alone can provide a compelling explanation for the observed patterns of SSD in Malagasy mammals.
Collapse
Affiliation(s)
- Peter M Kappeler
- Wissenschaftskolleg zu Berlin, Berlin, Germany.
- Behavioral Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute of Primatology, Göttingen, Germany.
- Department Sociobiology/Anthropology, University of Göttingen, Göttingen, Germany.
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Alexander Q Vining
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA
- Association Vahatra, Antananarivo, Madagascar
| |
Collapse
|
47
|
|
48
|
Fabre AC, Peckre L, Pouydebat E, Wall CE. Does the shape of forelimb long bones co-vary with grasping behaviour in strepsirrhine primates? Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
Fine prehensile activities are often thought to have been associated with the evolution of the human hand. However, there has been no holistic approach establishing the link between the morphology of the forelimb and grasping ability in living primates. The present study investigated the possible relationships between grasping behaviour and the morphology of the forelimb in strepsirrhines in a phylogenetic context. To do so, grasping behaviour during feeding and the shape of the long bones of the forelimb were analysed for 22 species of strepsirrhines. The data obtained show that there is a phylogenetic signal in forelimb morphology in primates in relation to grasping behaviour, but also that there is a marked co-evolution between grasping behaviour and the shape of the humerus and radius. This latter finding suggests a functional association between grasping and forelimb shape, which in turn suggests that bone shape constrains or facilitates behaviour. This result may permit future inferences to be made regarding this behaviour in extinct species and deserves further examination in more detail.
Collapse
Affiliation(s)
- Anne-Claire Fabre
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Evolutionary Anthropology, Duke University, Durham, USA
- UMR 7179 C.N.R.S., M.N.H.N. Département d’Ecologie et de Gestion de la Biodiversité, Muséum National d’Histoire Naturelle, Paris, France
| | - Louise Peckre
- UMR 7179 C.N.R.S., M.N.H.N. Département d’Ecologie et de Gestion de la Biodiversité, Muséum National d’Histoire Naturelle, Paris, France
- Behavioral Ecology & Sociobiology Unit, German Primate Center Leibniz Institute for Primate Research, Deutsches Primatenzentrum GmbH, Kellnerweg, Göttingen, Germany
| | - Emmanuelle Pouydebat
- UMR 7179 C.N.R.S., M.N.H.N. Département d’Ecologie et de Gestion de la Biodiversité, Muséum National d’Histoire Naturelle, Paris, France
| | - Christine E Wall
- Department of Evolutionary Anthropology, Duke University, Durham, USA
| |
Collapse
|
49
|
Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
Collapse
Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| |
Collapse
|
50
|
Fabre AC, Granatosky MC, Hanna JB, Schmitt D. Do forelimb shape and peak forces co-vary in strepsirrhines? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:602-614. [PMID: 30159895 DOI: 10.1002/ajpa.23688] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 06/07/2018] [Accepted: 07/07/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVES In this study, we explore whether ground reaction forces recorded during horizontal walking co-vary with the shape of the long bones of the forelimb in strepsirrhines. To do so, we quantify (1) the shape of the shaft and articular surfaces of each long bone of the forelimb, (2) the peak vertical, mediolateral, and horizontal ground reaction forces applied by the forelimb during arboreal locomotion, and (3) the relationship between the shape of the forelimb and peak forces. MATERIALS AND METHODS Geometric morphometric approaches were used to quantify the shape of the bones. Kinetic data were collected during horizontal arboreal walking in eight species of strepsirrhines that show variation in habitual substrate use and morphology of the forelimb. These data were then used to explore the links between locomotor behavior, morphology, and mechanics using co-variation analyses in a phylogenetic framework. RESULTS Our results show significant differences between slow quadrupedal climbers (lorises), vertical clinger and leapers (sifaka), and active arboreal quadrupeds (ring-tailed lemur, ruffed lemur) in both ground reaction forces and the shape of the long bones of the forelimb, with the propulsive and medially directed peak forces having the highest impact on the shape of the humerus. Co-variation between long bone shape and ground reaction forces was detected in both the humerus and ulna even when accounting for differences in body mass. DISCUSSION These results demonstrate the importance of considering limb-loading beyond just peak vertical force, or substrate reaction force. A re-evaluation of osseous morphology and functional interpretations is necessary in light of these findings.
Collapse
Affiliation(s)
- Anne-Claire Fabre
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
- UMR 7179 C.N.R.S., M.N.H.N. Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, Paris, France
| | - Michael C Granatosky
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
| | - Jandy B Hanna
- Department of Biomedical Science, West Virginia School of Osteopathic Medicine, Lewisburg, West Virginia
| | - Daniel Schmitt
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| |
Collapse
|