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Lambert S, Voznica J, Morlon H. Deep Learning from Phylogenies for Diversification Analyses. Syst Biol 2023; 72:1262-1279. [PMID: 37556735 DOI: 10.1093/sysbio/syad044] [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: 10/03/2022] [Revised: 06/20/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models, such a formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time-constant homogeneous BD model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for the deployment of future models in the field.
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Affiliation(s)
- Sophia Lambert
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
- Institute of Ecology and Evolution, Department of Biology, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Jakub Voznica
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 Rue du Dr Roux, 75015 Paris, France
- Unité de Biologie Computationnelle, USR 3756 CNRS, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 46 Rue d'Ulm, 75005 Paris, France
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2
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Liang X, Heath LS. Towards understanding paleoclimate impacts on primate de novo genes. G3 (BETHESDA, MD.) 2023; 13:jkad135. [PMID: 37313728 PMCID: PMC10468307 DOI: 10.1093/g3journal/jkad135] [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: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
De novo genes are genes that emerge as new genes in some species, such as primate de novo genes that emerge in certain primate species. Over the past decade, a great deal of research has been conducted regarding their emergence, origins, functions, and various attributes in different species, some of which have involved estimating the ages of de novo genes. However, limited by the number of species available for whole-genome sequencing, relatively few studies have focused specifically on the emergence time of primate de novo genes. Among those, even fewer investigate the association between primate gene emergence with environmental factors, such as paleoclimate (ancient climate) conditions. This study investigates the relationship between paleoclimate and human gene emergence at primate species divergence. Based on 32 available primate genome sequences, this study has revealed possible associations between temperature changes and the emergence of de novo primate genes. Overall, findings in this study are that de novo genes tended to emerge in the recent 13 MY when the temperature continues cooling, which is consistent with past findings. Furthermore, in the context of an overall trend of cooling temperature, new primate genes were more likely to emerge during local warming periods, where the warm temperature more closely resembled the environmental condition that preceded the cooling trend. Results also indicate that both primate de novo genes and human cancer-associated genes have later origins in comparison to random human genes. Future studies can be in-depth on understanding human de novo gene emergence from an environmental perspective as well as understanding species divergence from a gene emergence perspective.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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3
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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4
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Ji X, Harrison T, Zhang Y, Wu Y, Zhang C, Hu J, Wu D, Hou Y, Li S, Wang G, Wang Z. The earliest hylobatid from the Late Miocene of China. J Hum Evol 2022; 171:103251. [PMID: 36113226 DOI: 10.1016/j.jhevol.2022.103251] [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: 06/06/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/15/2022]
Abstract
Yuanmoupithecus xiaoyuan, a small catarrhine from the Late Miocene of Yunnan in southern China, was initially suggested to be related to Miocene proconsuloids or dendropithecoids from East Africa, but subsequent reports indicated that it might be more closely related to hylobatids. Here, detailed comparisons of the material, including seven newly discovered teeth and a partial lower face of a juvenile individual, provide crucial evidence to help establish its phylogenetic relationships. Yuanmoupithecus exhibits a suite of synapomorphies that support a close phylogenetic relationship with extant hylobatids. Furthermore, based on the retention of several primitive features of the dentition, Yuanmoupithecus can be shown to be the sister taxon of crown hylobatids. The contention that Kapi ramnagarensis from the Middle Miocene of India might represent an earlier species of hylobatid is not supported here. Instead, Kapi is inferred to be a specialized pliopithecoid more closely related to Krishnapithecus krishnaii from the Late Miocene of India. Currently then, Yuanmoupithecus represents the earliest known definitively identified hylobatid and the only member of the clade predating the Pleistocene. It extends the fossil record of hylobatids back to 7-8 Ma and fills a critical gap in the evolutionary history of hominoids that has up until now remained elusive. Even so, molecular estimates of a divergence date of hylobatids from other hominoids at about 17-22 Ma signifies that there is still a substantial gap in the fossil record of more than 10 million years that needs to be filled in order to document the biogeographic origins and early evolution of hylobatids.
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Affiliation(s)
- Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming, 650118, China
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, NY, 10003, USA.
| | - Yingqi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Yun Wu
- Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming, 650118, China; School of History, Wuhan University, Wuhan, 430072, China
| | - Chunxia Zhang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China; College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Jinming Hu
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650500, China
| | - Dongdong Wu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yemao Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guofu Wang
- Chuxiong Prefectural Museum, Chuxiong, 657000, China
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5
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The evolution of primate malaria parasites: A study on the origin and diversification of Plasmodium in lemurs. Mol Phylogenet Evol 2022; 174:107551. [PMID: 35690381 DOI: 10.1016/j.ympev.2022.107551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022]
Abstract
Among the primate malaria parasites, those found in lemurs have been neglected. Here, six Plasmodium lineages were detected in 169 lemurs. Nearly complete mitochondrial genomes (mtDNA, ≈6Kb) and apicoplast loci (≈6Kb) were obtained from these parasites and other Haemosporida species. Plasmodium spp. in lemurs are a diverse clade that shares a common ancestor with other primate parasites from continental Africa. Time-trees for the mtDNA were estimated under different scenarios, and the origin of the lemur clade coincides with the proposed time of their host species' most recent common ancestor (Lemuridae-Indriidae). A time tree with fewer taxa was estimated with mtDNA + Apicoplast loci. Those time estimates overlapped but were younger and had narrower credibility intervals than those from mtDNA alone. Importantly, the mtDNA + Apicoplast estimates that the clade including the most lethal malaria parasite in humans, Plasmodium falciparum, may have originated with Homininae (African apes). Finally, the phylogenetic congruence of the lemurs and their parasites was explored. A statistically significant scenario identified four cospeciation, two duplications, four transfer (host-switches), and zero loss events. Thus, the parasite species sampled in lemurs seem to be radiating with their hosts.
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6
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Valente D, Miaretsoa L, Anania A, Costa F, Mascaro A, Raimondi T, De Gregorio C, Torti V, Friard O, Ratsimbazafy J, Giacoma C, Gamba M. Comparative Analysis of the Vocal Repertoires of the Indri (Indri indri) and the Diademed Sifaka (Propithecus diadema). INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00287-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
AbstractStrepsirrhine vocalisations are extraordinarily diverse and cross-species comparisons are needed to explore how this variability evolved. We contributed to the investigation of primate acoustic diversity by comparing the vocal repertoire of two sympatric lemur species, Propithecus diadema and Indri indri. These diurnal species belong to the same taxonomic family and have similar activity patterns but different social structures. These features make them excellent candidates for an investigation of the phylogenetic, environmental, and social influence on primate vocal behavior. We recorded 3 P. diadema groups in 2014 and 2016. From 1,872 recordings we selected and assigned 3814 calls to 9 a priori call types, on the basis of their acoustic structure. We implemented a reproducible technique performing an acoustic feature extraction relying on frequency bins, t-SNE data reduction, and a hard-clustering analysis. We first quantified the vocal repertoire of P. diadema, finding consistent results for the 9 putatively identified call types. When comparing this repertoire with a previously published repertoire of I. indri, we found highly species-specific repertoires, with only 2% of the calls misclassified by species identity. The loud calls of the two species were very distinct, while the low-frequency calls were more similar. Our results pinpoint the role of phylogenetic history, social and environmental features on the evolution of communicative systems and contribute to a deeper understanding of the evolutionary roots of primate vocal differentiation. We conclude by arguing that standardized and reproducible techniques, like the one we employed, allow robust comparisons and should be prioritized in the future.
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7
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Pugh KD. Phylogenetic analysis of Middle-Late Miocene apes. J Hum Evol 2022; 165:103140. [DOI: 10.1016/j.jhevol.2021.103140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/18/2023]
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8
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Arenson JL, Harrison T, Sargis EJ, Taboada HG, Gilbert CC. A new species of fossil guenon (Cercopithecini, Cercopithecidae) from the Early Pleistocene Lower Ngaloba Beds, Laetoli, Tanzania. J Hum Evol 2022; 163:103136. [PMID: 35033736 DOI: 10.1016/j.jhevol.2021.103136] [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: 08/10/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
The living guenons (Cercopithecini, Cercopithecidae) are speciose and widely distributed across sub-Saharan Africa but are poorly represented in the fossil record. In addition, the craniodental and skeletal similarity of the guenons has hampered the identification of fragmentary material, likely obscuring the taxonomic diversity represented in the fossil record. Here, we describe a new fossil guenon specimen (LAET 75-3703) from the Lower Ngaloba Beds, Laetoli in Tanzania, dated to ∼1.7-1.2 Ma and preserving the lower face and mandible. Comparison to 278 extant guenon specimens, representing all six extant genera, identified several informative traits for distinguishing between the morphologically similar Chlorocebus and Cercopithecus, and these support the attribution of LAET 75-3703 to Chlorocebus. A discriminant function analysis of seven craniodental indices on a subsample of Chlorocebus and Cercopithecus was robust with an overall correct classification rate of 80.4%, and it classified LAET 75-3703 as a member of Chlorocebus with a posterior probability of 92.7%. LAET 75-3703 shares with Chlorocebus the presence of small 'thumbprint' depressions on the maxilla; a tall, narrow, and diamond-shaped nasal aperture; a relatively longer and shallower face; relatively buccolingually broader molars; and a shallow mandible that decreases in depth posteriorly. In addition, LAET 75-3703 is distinguished from all extant guenons, including other species of Chlorocebus, in having a very small P3 relative to M1 area. As such, LAET 75-3703 is assigned to a new species, Chlorocebus ngedere sp. nov. This specimen represents the first cercopithecin from Laetoli, as well as the oldest fossil cercopithecin confidently attributed to a modern genus.
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Affiliation(s)
- Julia L Arenson
- PhD Program in Anthropology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA; New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA.
| | - Terry Harrison
- New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA; Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA
| | - Eric J Sargis
- Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT, 06511, USA; Divisions of Vertebrate Paleontology and Vertebrate Zoology, Yale Peabody Museum of Natural History, 170 Whitney Avenue, New Haven, CT, 06511, USA; Yale Institute for Biospheric Studies, P.O. Box 208118, New Haven, CT, 06520, USA
| | - Hannah G Taboada
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA
| | - Christopher C Gilbert
- PhD Program in Anthropology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA; New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA; Department of Anthropology, Hunter College, CUNY, 695 Park Avenue, New York, NY, 10065, USA; Division of Paleontology, American Museum of Natural History, Central Park West, New York, NY, 10024, USA
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9
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Morel B, Schade P, Lutteropp S, Williams TA, Szöllősi GJ, Stamatakis A. SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss. Mol Biol Evol 2022; 39:6503503. [PMID: 35021210 PMCID: PMC8826479 DOI: 10.1093/molbev/msab365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paul Schade
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Gergely J Szöllősi
- ELTE-MTA "Lendület" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117 Budapest, Hungary.,Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117 Budapest, Hungary.,Institute of Evolution, Centre for Ecological Research, Konkoly-Thege M. út 29-33. H-1121 Budapest, Hungary
| | - Alexandros Stamatakis
- Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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10
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Srikulnath K, Ahmad SF, Panthum T, Malaivijitnond S. Importance of Thai macaque bioresources for biological research and human health. J Med Primatol 2021; 51:62-72. [PMID: 34806191 DOI: 10.1111/jmp.12555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/25/2023]
Abstract
During the past century, macaque bioresources have provided remarkable scientific and biomedical discoveries related to the understanding of human physiology, neuroanatomy, reproduction, development, cognition, and pathology. Considerable progress has been made, and an urgent need has arisen to develop infrastructure and viable settings to meet the current global demand in research models during the so-called new normal after COVID-19 era. This review highlights the critical need for macaque bioresources and proposes the establishment of a designated primate research center to integrate research in primate laboratories for the rescue and rehabilitation of wild macaques. Key areas where macaque models have been and continue to be essential for advancing fundamental knowledge in biomedical and biological research are outlined. Detailed genetic studies on macaque bioresources of Thai origin can further facilitate the rapid pace of vaccine discovery.
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Affiliation(s)
- Kornsorn Srikulnath
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand.,Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand.,Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand.,Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand.,Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand.,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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11
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Povill C, de Assis Passos Oliveira M, de Melo FR, Bonvicino CR. Phylogenetic relationships, population demography, and species delimitation of the Alouatta belzebul species complex (Atelidae: Alouattinae). Primates 2021; 63:65-78. [PMID: 34716855 DOI: 10.1007/s10329-021-00959-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/17/2021] [Indexed: 11/25/2022]
Abstract
Howler monkeys (genus Alouatta) exhibit the most extensive distribution among platyrrhines, comprising Mesoamerican and South American species groups, with the South American group including the Brazilian endemic A. belzebul species complex encompassing A. belzebul, A. discolor, and A. ululata. We herein analyzed their phylogenetic relationship, nucleotide and haplotype diversity, and population demography based on the mitochondrial gene cytochrome b. The phylogenetic and median-joining network analyses distinguished A. discolor, distributed in the west bank of the Xingu River, from A. belzebul on the east bank. This river is a zoogeographic barrier for these species. We did not find evidence of phylogenetic structure between the A. belzebul populations of opposite banks of the Tocantins River, likely related to the changes in the position of this river to the northeast in the late Pleistocene. The A. belzebul along this river showed great morphologic and haplotype diversity, and A. belzebul from the Amazon have kept a larger population size than A. discolor. We herein describe the karyotype of A. discolor, which was similar to those described for A. ululata and A. belzebul. Our results showed two well-defined and supported clades for A. discolor and A. belzebul. However, a new assessment of A. ululata across a large distribution of sampling is required due to the lack of a clear phylogenetic structure.
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Affiliation(s)
- Cintia Povill
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | | | - Cibele Rodrigues Bonvicino
- Genetics Program, National Cancer Institute, Rua André Cavalcanti, 37, 4°. Andar, Rio de Janeiro, Rio de Janeiro, 20231-050, Brazil.
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12
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Wertheim JO, Hostager R, Ryu D, Merkel K, Angedakin S, Arandjelovic M, Ayimisin EA, Babweteera F, Bessone M, Brun-Jeffery KJ, Dieguez P, Eckardt W, Fruth B, Herbinger I, Jones S, Kuehl H, Langergraber KE, Lee K, Madinda NF, Metzger S, Ormsby LJ, Robbins MM, Sommer V, Stoinski T, Wessling EG, Wittig RM, Yuh YG, Leendertz FH, Calvignac-Spencer S. Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2. Mol Biol Evol 2021; 38:2818-2830. [PMID: 33720357 PMCID: PMC8233514 DOI: 10.1093/molbev/msab072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Reilly Hostager
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Diane Ryu
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Kevin Merkel
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | | | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Winnie Eckardt
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Barbara Fruth
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Royal Society for the Protection of Birds, Centre for Conservation Science, Cambridge, United Kingdom
| | - Hjalmar Kuehl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Nadege F Madinda
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sonja Metzger
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Volker Sommer
- Department of Anthropology, University College London, London, United Kingdom.,Gashaka Primate Project, Serti/Taraba, Nigeria
| | - Tara Stoinski
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Erin G Wessling
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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13
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New Insights on the Evolution of the Sweet Taste Receptor of Primates Adapted to Harsh Environments. Animals (Basel) 2020; 10:ani10122359. [PMID: 33321745 PMCID: PMC7764350 DOI: 10.3390/ani10122359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary A sense of taste is vital to an animal’s fitness. It enables animals to select and ingest beneficial foods and avoid harmful substances in their daily lives. There have been relatively few studies regarding the evolution of the taste receptor gene for sweetness, particularly in regard to endemic Bornean primates. We constructed TAS1R2 gene phylogenies for 20 anthropoid primate species using four different methods as well as established the phylogenic time divergence. The phylogenetic analysis successfully separated the primates into their taxonomic groups and as per their dietary preferences. Of note, the estimated time of divergence for the primate speciation pattern in this study was more recent than the previously published estimates. This difference may have been due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which likely forced primates to adapt their dietary preferences. These findings establish a foundation for further investigations. Abstract Taste perception is an essential function that provides valuable dietary and sensory information, which is crucial for the survival of animals. Studies into the evolution of the sweet taste receptor gene (TAS1R2) are scarce, especially for Bornean endemic primates such as Nasalis larvatus (proboscis monkey), Pongo pygmaeus (Bornean orangutan), and Hylobates muelleri (Muller’s Bornean gibbon). Primates are the perfect taxa to study as they are diverse dietary feeders, comprising specialist folivores, frugivores, gummivores, herbivores, and omnivores. We constructed phylogenetic trees of the TAS1R2 gene for 20 species of anthropoid primates using four different methods (neighbor-joining, maximum parsimony, maximum-likelihood, and Bayesian) and also established the time divergence of the phylogeny. The phylogeny successfully separated the primates into their taxonomic groups as well as by their dietary preferences. Of note, the reviewed time of divergence estimation for the primate speciation pattern in this study was more recent than the previously published estimates. It is believed that this difference may be due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which forced primates to change their dietary preferences. These findings provide a starting point for further investigation.
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14
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Carter CS, Richardson A, Huffman DM, Austad S. Bring Back the Rat! J Gerontol A Biol Sci Med Sci 2020; 75:405-415. [PMID: 31894235 DOI: 10.1093/gerona/glz298] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 12/12/2022] Open
Abstract
As 2020 is "The Year of the Rat" in the Chinese astrological calendar, it seems an appropriate time to consider whether we should bring back the laboratory rat to front-and-center in research on the basic biology of mammalian aging. Beginning in the 1970s, aging research with rats became common, peaking in 1992 but then declined dramatically by 2018 as the mouse became preeminent. The purpose of this review is to highlight some of the historical contributions as well as current advantages of the rat as a mammalian model of human aging, because we suspect at least a generation of researchers is no longer aware of this history or these advantages. Herein, we compare and contrast the mouse and rat in the context of several biological domains relevant to their use as appropriate models of aging: phylogeny/domestication, longevity interventions, pathology/physiology, and behavior/cognition. It is not the goal of this review to give a complete characterization of the differences between mice and rats, but to provide important examples of why using rats as well as mice is important to advance our understanding of the biology of aging.
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Affiliation(s)
- Christy S Carter
- Department of Medicine, Division of Gerontology, Geriatrics and Palliative Care, School of Medicine, University of Alabama at Birmingham
| | - Arlan Richardson
- Department of Biochemistry and Molecular Biology, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Science Center, and the Oklahoma City VA Medical Center
| | - Derek M Huffman
- Department of Molecular Pharmacology, Department of Medicine, and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, New York
| | - Steven Austad
- Department of Biology, College of Arts and Sciences, University of Alabama at Birmingham
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15
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Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues. mBio 2020; 11:mBio.02772-20. [PMID: 33203760 PMCID: PMC7683403 DOI: 10.1128/mbio.02772-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Organisms can access genetic and functional novelty by capturing viral elements within their genomes, where they can evolve to drive new cellular or organismal processes. We demonstrate that a retroviral envelope gene, EnvP(b)1, has been maintained and its fusion activity preserved for 40 to 71 million years. It is expressed as a protein in multiple healthy human tissues. We determined the structure of its inferred receptor binding domain and compared it with the same domain in modern viruses. We found a common conserved architecture that underlies the varied receptor binding activity of divergent Env genes. The modularity and versatility of this domain may underpin the evolutionary success of this clade of fusogens. EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.
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16
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Comparing Rates of Linage Diversification with Rates of Size and Shape Evolution in Catarrhine Crania. Evol Biol 2020. [DOI: 10.1007/s11692-020-09500-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Dong C, Duan X, Younis LM, Zhang M, Ma X, Chen B, Li X, Xu P. Mitogenomic Perspectives on the Adaptation to Extreme Alkaline Environment of Amur ide (Leuciscus waleckii). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:220-232. [PMID: 32030579 DOI: 10.1007/s10126-020-09946-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Amur ide (Leuciscus waleckii, Family Cyprinidae) is widely distributed in Northeast Asia. L. waleckii usually inhabits freshwater environments but can also survive in the Lake Dali Nur, one of the most extreme aquatic environments on the earth, with an alkalinity up to 50 mmol/L (pH 9.6). To investigate mechanisms of mitogenomic evolution underlying adaptation to extreme environments, we determined 30 complete mitogenomes that included Lake Dali Nur (alkaline environment, AL) population and Amur basin (freshwater environment, FW) population. Through phylogenetic and divergence time analysis, we found that AL and FW populations forming distinct two groups which were consistent with geographic divergence (the formation of Lake Dali Nur). In addition, we found that almost of the windows exhibited higher nucleotide diversity in FW population (avg 0.0046) than AL population (avg 0.0012). This result indicated that severe environment selection had remarkably reduced the genetic diversity of mitogenome in AL population and suggested that severe environment selection had remarkably reduced the genetic diversity of mitogenome in the AL population. Compared with the FW population (ω = 0.064), the AL population (ω = 0.092) had a larger mean ω (dN/dS ratios) value for the 13 concatenated mitochondrial protein-coding genes, indicating that the high alkaline tolerated group had accumulated more nonsynonymous mutations. These nonsynonymous mutations had resulted in slightly beneficial amino acid changes that allowed adaption to the severe conditions. This study provides an additional view to decipher the adaptive mitogenome evolution of L. waleckii of the high alkaline environment.
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Affiliation(s)
- Chuanju Dong
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China
- Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro, Sindh, 76080, Pakistan
| | - Xiaodi Duan
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China
| | - Laghari Muhammad Younis
- Department of Fresh Water Biology and Fisheries, University of Sindh, Jamshoro, Sindh, 76080, Pakistan
| | - Meng Zhang
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xiao Ma
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China
| | - Baohua Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Xuejun Li
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Peng Xu
- College of Fishery Henan Normal University, Xinxiang, 453007, Henan, China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
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18
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Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, Ploss A. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance 2019; 2:2/5/e201900495. [PMID: 31649152 PMCID: PMC6814850 DOI: 10.26508/lsa.201900495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/03/2023] Open
Abstract
The transcriptomic response of diverse nonhuman primate (NHP) species to poly(I:C) is highly conserved, and this novel RNA sequencing dataset will help improve NHP genome annotations. Differences in immune responses across species can contribute to the varying permissivity of species to the same viral pathogen. Understanding how our closest evolutionary relatives, nonhuman primates (NHPs), confront pathogens and how these responses have evolved over time could shed light on host range barriers, especially for zoonotic infections. Here, we analyzed cell-intrinsic immunity of primary cells from the broadest panel of NHP species interrogated to date, including humans, great apes, and Old and New World monkeys. Our analysis of their transcriptomes after poly(I:C) transfection revealed conservation in the functional consequences of their response. In mapping reads to either the human or the species-specific genomes, we observed that with the current state of NHP annotations, the percent of reads assigned to a genetic feature was largely similar regardless of the method. Together, these data provide a baseline for the cell-intrinsic responses elicited by a potent immune stimulus across multiple NHP donors, including endangered species, and serve as a resource for refining and furthering the existing annotations of NHP genomes.
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Affiliation(s)
- Jenna M Gaska
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Lance Parsons
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Metodi Balev
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ann Cirincione
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Robert E Schwartz
- Weill Cornell Medical College, Belfer Research Building, New York, NY, USA
| | - Alexander Ploss
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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19
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Rooker K, Gavrilets S. On the evolution of visual female sexual signalling. Proc Biol Sci 2019; 285:rspb.2017.2875. [PMID: 29848642 DOI: 10.1098/rspb.2017.2875] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/30/2018] [Indexed: 11/12/2022] Open
Abstract
A long-standing evolutionary puzzle surrounds female sexual signals visible around the time of ovulation. Even among just primates, why do some species have substantial sexual swellings and/or bright colorations visible around females' genital regions, while other species are like humans, with no signs of ovulation visible? What is the evolutionary purpose behind not just these signs, but also this great variation seen among species? Here, we examine the evolutionary trade-offs associated with visual ovulation signalling using agent-based modelling. Our model predicts how various factors, including male genetic heterogeneity and reproductive inequality, female physiological costs, group size, and the weighting of genetic versus non-genetic benefits coming from males, each influence the strength of ovulation signalling. Our model also predicts that increasing the impacts of infanticide will increase ovulation signalling. We use comparative primate data to show that, as predicted by our model, larger group size and higher risk of infanticide each correlate with having stronger visual ovulation signs. Overall, our work resolves some old controversies and sheds new light on the evolution of visual female sexual signalling.
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Affiliation(s)
- Kelly Rooker
- Department of Mathematics, University of Tennessee, Knoxville, TN 37996, USA
| | - Sergey Gavrilets
- Department of Mathematics, University of Tennessee, Knoxville, TN 37996, USA .,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996, USA
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20
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Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2019; 35:518-522. [PMID: 29077904 PMCID: PMC5850222 DOI: 10.1093/molbev/msx281] [Citation(s) in RCA: 3961] [Impact Index Per Article: 792.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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Affiliation(s)
- Diep Thi Hoang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
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21
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Eyun SI. Accelerated pseudogenization of trace amine-associated receptor genes in primates. GENES BRAIN AND BEHAVIOR 2019; 18:e12543. [PMID: 30536583 PMCID: PMC6849804 DOI: 10.1111/gbb.12543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023]
Abstract
Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine‐associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species‐specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity.
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Affiliation(s)
- Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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22
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ORTIZ ALEJANDRA, ZHANG YINGQI, JIN CHANGZHU, WANG YUAN, ZHU MIN, YAN YALING, KIMOCK CLARE, VILLAMIL CATALINAI, HE KAI, HARRISON TERRY. Morphometric analysis of fossil hylobatid molars from the Pleistocene of southern China. ANTHROPOL SCI 2019. [DOI: 10.1537/ase.190331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- ALEJANDRA ORTIZ
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe
| | - YINGQI ZHANG
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, Beijing
- CAS Center for Excellence in Life and Paleoenvironment, Beijing
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing
| | - CHANGZHU JIN
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, Beijing
- CAS Center for Excellence in Life and Paleoenvironment, Beijing
| | - YUAN WANG
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, Beijing
- CAS Center for Excellence in Life and Paleoenvironment, Beijing
| | - MIN ZHU
- School of History, Beijing Normal University, Beijing
| | - YALING YAN
- The Geoscience Museum, Hebei GEO University, Shijiazhuang
| | - CLARE KIMOCK
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York
- New York Consortium in Evolutionary Primatology, New York
| | | | - KAI HE
- School of Basic Medical Sciences, Southern Medical University, Guangzhou
| | - TERRY HARRISON
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York
- New York Consortium in Evolutionary Primatology, New York
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23
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Wang X, Lim BK, Ting N, Hu J, Liang Y, Roos C, Yu L. Reconstructing the phylogeny of new world monkeys ( platyrrhini): evidence from multiple non-coding loci. Curr Zool 2018; 65:579-588. [PMID: 31616489 PMCID: PMC6784508 DOI: 10.1093/cz/zoy072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/12/2018] [Indexed: 11/27/2022] Open
Abstract
Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.
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Affiliation(s)
- Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yunpeng Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg, Göttingen, Germany
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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24
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Scott JE. Reevaluating cases of trait-dependent diversification in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:244-256. [DOI: 10.1002/ajpa.23621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/23/2018] [Accepted: 05/12/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific; Western University of Health Sciences; Pomona California 91766
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25
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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26
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Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2018. [PMID: 29077904 DOI: 10.5281/zenodo.854445] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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Affiliation(s)
- Diep Thi Hoang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
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27
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Phylogeny mandalas for illustrating the Tree of Life. Mol Phylogenet Evol 2017; 117:168-178. [DOI: 10.1016/j.ympev.2016.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
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28
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Worthington S. Selection of Character Coding Method Is Not Phylogenetically Neutral: A Test Case Using Hominoids. Folia Primatol (Basel) 2017; 88:385-400. [PMID: 29130999 DOI: 10.1159/000479427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The early stages of phylogenetic inference from morphological data involve a sequence of choices about which analytical methods to employ. At each stage, the selection of one method over another can dramatically impact tree inference. Phylogenetic hypotheses are sensitive to decisions relating to which taxa and characters to select for analysis, whether and how to delimit character states, which taxa to use as outgroups, and how to account for character dependence. Using extant hominoids as a test case, I quantify the degree to which phylogenetic inferences are sensitive to the choice of method used to transform continuously scaled variables into categorical traits. I demonstrate that the character coding strategy significantly impacts hypotheses of character state identity and phylogenetic branching patterns. To avoid biasing evolutionary hypotheses, I recommend that continuously scaled characters be analyzed without prior discretization.
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Affiliation(s)
- Steven Worthington
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
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29
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Schmitt K, Mohan Kumar D, Curlin J, Remling-Mulder L, Stenglein M, O'Connor S, Marx P, Akkina R. Modeling the evolution of SIV sooty mangabey progenitor virus towards HIV-2 using humanized mice. Virology 2017; 510:175-184. [PMID: 28750321 PMCID: PMC5906053 DOI: 10.1016/j.virol.2017.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 11/27/2022]
Abstract
HIV-2 is thought to have originated from an SIV progenitor native to sooty mangabeys. To model the initial human transmission and understand the sequential viral evolution, humanized mice were infected with SIVsm and serially passaged for five generations. Productive infection was seen by week 3 during the initial challenge followed by chronic viremia and gradual CD4+ T cell decline. Viral loads increased by the 5th generation resulting in more rapid CD4+ T cell decline. Genetic analysis revealed several amino acid substitutions that were nonsynonymous and fixed in multiple hu-mice across each of the 5 generations in the nef, env and rev regions. The highest rate of substitution occurred in the nef and env regions and most were observed within the first two generations. These data demonstrated the utility of hu-mice in modeling the SIVsm transmission to the human and to evaluate its potential sequential evolution into a human pathogen of HIV-2 lineage.
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Affiliation(s)
- Kimberly Schmitt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dipu Mohan Kumar
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - James Curlin
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Leila Remling-Mulder
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Shelby O'Connor
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Preston Marx
- Department of Tropical Medicine, School Public Health and Tropical Medicine, New Orleans, LA 70112, USA; Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Ramesh Akkina
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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30
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Yang GD, Agapow PM, Yedid G. The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation. PLoS One 2017. [PMID: 28644846 PMCID: PMC5482465 DOI: 10.1371/journal.pone.0179553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.
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Affiliation(s)
- Guan-Dong Yang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul-Michael Agapow
- Data Science Institute, William Penney Laboratory, Imperial College, South Kensington, London, United Kingdom
| | - Gabriel Yedid
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- * E-mail:
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31
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Variation in gaze-following between two Asian colobine monkeys. Primates 2017; 58:525-534. [PMID: 28540427 DOI: 10.1007/s10329-017-0612-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 05/10/2017] [Indexed: 02/06/2023]
Abstract
Gaze-following is a basic cognitive ability found in numerous primate and nonprimate species. However, little is known about this ability and its variation in colobine monkeys. We compared gaze-following of two Asian colobines-François' langurs (Trachypithecus francoisi) and golden snub-nosed monkeys (Rhinopithecus roxellana). Although both species live in small polygynous family units, units of the latter form multilevel societies with up to hundreds of individuals. François' langurs (N = 15) were less sensitive to the gaze of a human experimenter than were golden snub-nosed monkeys (N = 12). We then tested the two species using two classic inhibitory control tasks-the cylinder test and the A-not-B test. We found no difference between species in inhibitory control, which called into question the nonsocial explanation for François' langur's weaker sensitivity to human gaze. These findings are consistent with the social intelligence hypothesis, which predicted that golden snub-nosed monkeys would outperform François' langurs in gaze-following because of the greater size and complexity of their social groups. Furthermore, our results underscore the need for more comparative studies of cognition in colobines, which should provide valuable opportunities to test hypotheses of cognitive evolution.
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32
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Tavares WC, Seuánez HN. Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PLoS One 2017; 12:e0177403. [PMID: 28510580 PMCID: PMC5433710 DOI: 10.1371/journal.pone.0177403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/26/2017] [Indexed: 01/09/2023] Open
Abstract
Several human diseases have been associated with mutations in mitochondrial genes comprising a set of confirmed and reported mutations according to the MITOMAP database. An analysis of complete mitogenomes across 139 primate species showed that most confirmed disease-associated mutations occurred in aligned codon positions and gene regions under strong purifying selection resulting in a strong evolutionary conservation. Only two confirmed variants (7.1%), coding for the same amino acids accounting for severe human diseases, were identified without apparent pathogenicity in non-human primates, like the closely related Bornean orangutan. Conversely, reported disease-associated mutations were not especially concentrated in conserved codon positions, and a large fraction of them occurred in highly variable ones. Additionally, 88 (45.8%) of reported mutations showed similar variants in several non-human primates and some of them have been present in extinct species of the genus Homo. Considering that recurrent mutations leading to persistent variants throughout the evolutionary diversification of primates are less likely to be severely damaging to fitness, we suggest that these 88 mutations are less likely to be pathogenic. Conversely, 69 (35.9%) of reported disease-associated mutations occurred in extremely conserved aligned codon positions which makes them more likely to damage the primate mitochondrial physiology.
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Affiliation(s)
- William Corrêa Tavares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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33
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Arbour JH, Santana SE. A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity. Evolution 2017; 71:1600-1613. [PMID: 28346661 DOI: 10.1111/evo.13237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/12/2017] [Indexed: 01/11/2023]
Abstract
Primates represent one of the most species rich, wide ranging, and ecologically diverse clades of mammals. What major macroevolutionary factors have driven their diversification and contributed to the modern distribution of primate species remains widely debated. We employed phylogenetic comparative methods to examine the role of clade age and evolutionary rate heterogeneity in the modern distribution of species diversity of Primates. Primate diversification has accelerated since its origin, with decreased extinction leading to a shift to even higher evolutionary rates in the most species rich family (Cercopithecidae). Older primate clades tended to be more diverse, however a shift in evolutionary rate was necessary to adequately explain the imbalance in species diversity. Species richness was also poorly explained by geographic distribution, especially once clade age and evolutionary rate shifts were accounted for, and may relate instead to other ecological factors. The global distribution of primate species diversity appears to have been strongly impacted by heterogeneity in evolutionary rates.
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Affiliation(s)
- Jessica H Arbour
- Department of Biology, University of Washington, Seattle, Washington, 98195
| | - Sharlene E Santana
- Department of Biology, University of Washington, Seattle, Washington, 98195.,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195
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34
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Masters JC, Génin F, Couette S, Groves CP, Nash SD, Delpero M, Pozzi L. A new genus for the eastern dwarf galagos (Primates: Galagidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw028] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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35
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St. Clair EM, Boyer DM. Lower molar shape and size in prosimian and platyrrhine primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:237-58. [DOI: 10.1002/ajpa.23021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/12/2016] [Accepted: 05/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth M. St. Clair
- Center for Functional Anatomy and EvolutionJohns Hopkins UniversityBaltimore Maryland21205
| | - Doug M. Boyer
- Department of Evolutionary AnthropologyDuke UniversityDurham North Carolina27708
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36
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Phylogenetic signal in molar dental shape of extant and fossil catarrhine primates. J Hum Evol 2016; 94:13-27. [DOI: 10.1016/j.jhevol.2016.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 09/28/2015] [Accepted: 01/23/2016] [Indexed: 11/17/2022]
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37
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Chernomor O, von Haeseler A, Minh BQ. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst Biol 2016; 65:997-1008. [PMID: 27121966 PMCID: PMC5066062 DOI: 10.1093/sysbio/syw037] [Citation(s) in RCA: 939] [Impact Index Per Article: 117.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 11/13/2022] Open
Abstract
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.
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Affiliation(s)
- Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Vienna, Austria and
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Vienna, Austria and.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Vienna, Austria and
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38
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Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
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39
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Kasperski A, Kasperska R. A new approach to the automatic identification of organism evolution using neural networks. Biosystems 2016; 142-143:32-42. [PMID: 26975238 DOI: 10.1016/j.biosystems.2016.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/20/2016] [Accepted: 03/08/2016] [Indexed: 12/30/2022]
Abstract
Automatic identification of organism evolution still remains a challenging task, which is especially exiting, when the evolution of human is considered. The main aim of this work is to present a new idea to allow organism evolution analysis using neural networks. Here we show that it is possible to identify evolution of any organisms in a fully automatic way using the designed EvolutionXXI program, which contains implemented neural network. The neural network has been taught using cytochrome b sequences of selected organisms. Then, analyses have been carried out for the various exemplary organisms in order to demonstrate capabilities of the EvolutionXXI program. It is shown that the presented idea allows supporting existing hypotheses, concerning evolutionary relationships between selected organisms, among others, Sirenia and elephants, hippopotami and whales, scorpions and spiders, dolphins and whales. Moreover, primate (including human), tree shrew and yeast evolution has been reconstructed.
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Affiliation(s)
- Andrzej Kasperski
- Faculty of Biological Sciences, Department of Biotechnology, University of Zielona Gora, ul. Szafrana 1, 65-516 Zielona Gora, Poland.
| | - Renata Kasperska
- Institute of Occupational Safety Engineering and Work Science, University of Zielona Gora, ul. Szafrana 4, 65-516 Zielona Gora, Poland
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40
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Roos C. Phylogeny and Classification of Gibbons (Hylobatidae). DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Harrison T. The Fossil Record and Evolutionary History of Hylobatids. DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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42
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Senter P, Moch JG. A critical survey of vestigial structures in the postcranial skeletons of extant mammals. PeerJ 2015; 3:e1439. [PMID: 26623192 PMCID: PMC4662599 DOI: 10.7717/peerj.1439] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/04/2015] [Indexed: 11/20/2022] Open
Abstract
In the Mammalia, vestigial skeletal structures abound but have not previously been the focus of study, with a few exceptions (e.g., whale pelves). Here we use a phylogenetic bracketing approach to identify vestigial structures in mammalian postcranial skeletons and present a descriptive survey of such structures in the Mammalia. We also correct previous misidentifications, including the previous misidentification of vestigial caviid metatarsals as sesamoids. We also examine the phylogenetic distribution of vestigiality and loss. This distribution indicates multiple vestigialization and loss events in mammalian skeletal structures, especially in the hand and foot, and reveals no correlation in such events between mammalian fore and hind limbs.
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Affiliation(s)
- Phil Senter
- Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, United States
| | - John G. Moch
- Department of Chemistry and Physics, Fayetteville State University, Fayetteville, NC, United States
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43
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Dececchi TA, Balhoff JP, Lapp H, Mabee PM. Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Syst Biol 2015; 64:936-52. [PMID: 26018570 PMCID: PMC4604830 DOI: 10.1093/sysbio/syv031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/20/2015] [Indexed: 02/02/2023] Open
Abstract
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
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Affiliation(s)
| | - James P Balhoff
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA;
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44
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Neutral Theory Overestimates Extinction Times in Nonhuman Primates. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Masters JC, Couette S. Characterizing cryptic species: A morphometric analysis of craniodental characters in the dwarf galago genusGalagoides. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:288-299. [DOI: 10.1002/ajpa.22792] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/28/2015] [Accepted: 05/28/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Judith C. Masters
- African Primate Initiative for Ecology and Speciation; Department of Zoology and Entomology; University of Fort Hare; Private Bag X1314 Alice 5700 South Africa
| | - Sébastien Couette
- Ecole Pratique des Hautes Etudes; Laboratoire Paléobiodiversité et Evolution & UMR uB CNRS 6282 «Biogéosciences»; Université de Bourgogne; 6 Bld Gabriel Dijon 21000 France
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46
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Ortiz A, Pilbrow V, Villamil CI, Korsgaard JG, Bailey SE, Harrison T. The Taxonomic and Phylogenetic Affinities of Bunopithecus sericus, a Fossil Hylobatid from the Pleistocene of China. PLoS One 2015; 10:e0131206. [PMID: 26154175 PMCID: PMC4495929 DOI: 10.1371/journal.pone.0131206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
Fossil hylobatids are rare, but are known from late Miocene and Pleistocene sites throughout East Asia. The best-known fossil hylobatid from the Pleistocene of China is a left mandibular fragment with M2-3 (AMNH 18534), recovered from a pit deposit near the village of Yanjinggou in Wanzhou District, Chongqing Province. Matthew and Granger described this specimen in 1923 as a new genus and species, Bunopithecus sericus. Establishing the age of Bunopithecus has proved difficult because the Yanjinggou collection represents a mixed fauna of different ages, but it likely comes from early or middle Pleistocene deposits. Although the Bunopithecus specimen has featured prominently in discussions of hylobatid evolution and nomenclature, its systematic status has never been satisfactorily resolved. The present study reexamines the taxonomic and phylogenetic relationships of Bunopithecus by carrying out a detailed comparative morphometric study of its lower molars in relation to a large sample of modern hylobatids. Our results show that differences in M2 and M3 discriminate extant hylobatids fairly well, at least at the generic level, and that AMNH 18534 is not attributable to Hylobates, Nomascus or Symphalangus. Support for a close relationship between Bunopithecus and Hoolock is more equivocal. In most multivariate analyses, Bunopithecus presents a unique morphological pattern that falls outside the range of variation of any hylobatid taxon, although its distance from the cluster represented by extant hoolocks is relatively small. Our results support the generic distinction of Bunopithecus, which most likely represents an extinct crown hylobatid, and one that may possibly represent the sister taxon to Hoolock.
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Affiliation(s)
- Alejandra Ortiz
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
| | - Varsha Pilbrow
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, Australia
| | - Catalina I. Villamil
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
| | - Jessica G. Korsgaard
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, New York, United States of America
| | - Shara E. Bailey
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, United States of America
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Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biol Evol 2015; 7:1988-99. [PMID: 26133389 PMCID: PMC4524488 DOI: 10.1093/gbe/evv121] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes.
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Affiliation(s)
| | - Marina Marcet-Houben
- Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain
| | - Jonathan A Rees
- US National Evolutionary Synthesis Center, Duke University, Durham, NC
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ioannis Xenarios
- Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit, University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | | | - Toni Gabaldón
- Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain
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48
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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49
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Pozzi L, Nekaris KAI, Perkin A, Bearder SK, Pimley ER, Schulze H, Streicher U, Nadler T, Kitchener A, Zischler H, Zinner D, Roos C. Remarkable ancient divergences amongst neglected lorisiform primates. Zool J Linn Soc 2015; 175:661-674. [PMID: 26900177 PMCID: PMC4744660 DOI: 10.1111/zoj.12286] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 11/29/2022]
Abstract
Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub-Saharan Africa and South/South-East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group.
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Affiliation(s)
- Luca Pozzi
- Behavioral Ecology and Sociobiology Unit German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
| | | | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes UniversityOxfordOX3 0BPUK; Tanzania Forest Conservation GroupPO Box 23410Dar es SalaamTanzania
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University Oxford OX3 0BP UK
| | - Elizabeth R Pimley
- Nocturnal Primate Research Group, Oxford Brookes UniversityOxfordOX3 0BPUK; School of Natural & Social SciencesUniversity of GloucestershireFrancis Close HallSwindon RoadCheltenhamGloucestershireGL50 4AZUK
| | - Helga Schulze
- Department of Neuroanatomy MA 01/43 Ruhr University 44780 Bochum Germany
| | | | - Tilo Nadler
- Endangered Primate Rescue Center, Cuc Phuong National Park Nho Quan District, Ninh Binh Province Vietnam
| | - Andrew Kitchener
- Department of Natural SciencesNational Museums ScotlandChambers StreetEdinburghEH1 1JFUK; Institute of GeographySchool of GeoSciencesUniversity of EdinburghDrummond StreetEdinburghEH8 9XPUK
| | - Hans Zischler
- Institute of Anthropology University of Mainz Anselm-Franz-von-Bentzel-Weg 7 55128 Mainz Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory German Primate Center, Leibniz Institute for Primate Research Kellnerweg 4 37077 Göttingen Germany
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50
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Wroblewski EE, Norman PJ, Guethlein LA, Rudicell RS, Ramirez MA, Li Y, Hahn BH, Pusey AE, Parham P. Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz. PLoS Biol 2015; 13:e1002144. [PMID: 26020813 PMCID: PMC4447270 DOI: 10.1371/journal.pbio.1002144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules determine immune responses to viral infections. These polymorphic cell-surface glycoproteins bind peptide antigens, forming ligands for cytotoxic T and natural killer cell receptors. Under pressure from rapidly evolving viruses, hominoid MHC class I molecules also evolve rapidly, becoming diverse and species-specific. Little is known of the impact of infectious disease epidemics on MHC class I variant distributions in human populations, a context in which the chimpanzee is the superior animal model. Population dynamics of the chimpanzees inhabiting Gombe National Park, Tanzania have been studied for over 50 years. This population is infected with SIVcpz, the precursor of human HIV-1. Because HLA-B is the most polymorphic human MHC class I molecule and correlates strongly with HIV-1 progression, we determined sequences for its ortholog, Patr-B, in 125 Gombe chimpanzees. Eleven Patr-B variants were defined, as were their frequencies in Gombe's three communities, changes in frequency with time, and effect of SIVcpz infection. The growing populations of the northern and central communities, where SIVcpz is less prevalent, have stable distributions comprising a majority of low-frequency Patr-B variants and a few high-frequency variants. Driving the latter to high frequency has been the fecundity of immigrants to the northern community, whereas in the central community, it has been the fecundity of socially dominant individuals. In the declining population of the southern community, where greater SIVcpz prevalence is associated with mortality and emigration, Patr-B variant distributions have been changing. Enriched in this community are Patr-B variants that engage with natural killer cell receptors. Elevated among SIVcpz-infected chimpanzees, the Patr-B*06:03 variant has striking structural and functional similarities to HLA-B*57, the human allotype most strongly associated with delayed HIV-1 progression. Like HLA-B*57, Patr-B*06:03 correlates with reduced viral load, as assessed by detection of SIVcpz RNA in feces.
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Affiliation(s)
- Emily E. Wroblewski
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rebecca S. Rudicell
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Sanofi, Cambridge, Massachusetts, United States of America
| | - Miguel A. Ramirez
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
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