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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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2
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Schwartz JW, Gouzoules H. Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication. PeerJ 2022; 10:e14471. [PMID: 36518288 PMCID: PMC9744152 DOI: 10.7717/peerj.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 12/05/2022] Open
Abstract
Humans and other mammalian species communicate emotions in ways that reflect evolutionary conservation and continuity, an observation first made by Darwin. One approach to testing this hypothesis has been to assess the capacity to perceive the emotional content of the vocalizations of other species. Using a binary forced choice task, we tested perception of the emotional intensity represented in coos and screams of infant and juvenile female rhesus macaques (Macaca mulatta) by 113 human listeners without, and 12 listeners with, experience (as researchers or care technicians) with this species. Each stimulus pair contained one high- and one low-arousal vocalization, as measured at the time of recording by stress hormone levels for coos and the degree of intensity of aggression for screams. For coos as well as screams, both inexperienced and experienced participants accurately identified the high-arousal vocalization at significantly above-chance rates. Experience was associated with significantly greater accuracy with scream stimuli but not coo stimuli, and with a tendency to indicate screams as reflecting greater emotional intensity than coos. Neither measures of empathy, human emotion recognition, nor attitudes toward animal welfare showed any relationship with responses. Participants were sensitive to the fundamental frequency, noisiness, and duration of vocalizations; some of these tendencies likely facilitated accurate perceptions, perhaps due to evolutionary homologies in the physiology of arousal and vocal production between humans and macaques. Overall, our findings support a view of evolutionary continuity in emotional vocal communication. We discuss hypotheses about how distinctive dimensions of human nonverbal communication, like the expansion of scream usage across a range of contexts, might influence perceptions of other species' vocalizations.
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Affiliation(s)
- Jay W. Schwartz
- Department of Psychology, Emory University, Atlanta, GA, United States,Psychological Sciences Department, Western Oregon University, Monmouth, OR, United States
| | - Harold Gouzoules
- Department of Psychology, Emory University, Atlanta, GA, United States
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3
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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4
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Bergeron LA, Besenbacher S, Bakker J, Zheng J, Li P, Pacheco G, Sinding MHS, Kamilari M, Gilbert MTP, Schierup MH, Zhang G. The germline mutational process in rhesus macaque and its implications for phylogenetic dating. Gigascience 2021; 10:giab029. [PMID: 33954793 PMCID: PMC8099771 DOI: 10.1093/gigascience/giab029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
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Affiliation(s)
- Lucie A Bergeron
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark
| | - Jaco Bakker
- Animal Science Department, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Panyi Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mikkel-Holger S Sinding
- Department of genetics, Trinity College Dublin, 2 college green, D02 VF25, Dublin, Ireland
- Greenland Institute of Natural Resources, Kivioq 2, 3900 Nuuk, Greenland
| | - Maria Kamilari
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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5
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Chintalapati M, Moorjani P. Evolution of the mutation rate across primates. Curr Opin Genet Dev 2020; 62:58-64. [PMID: 32634682 DOI: 10.1016/j.gde.2020.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/10/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Germline mutations are the source of all heritable variation. In the past few years, whole genome sequencing has allowed direct and comprehensive surveys of mutation patterns in humans and other species. These studies have documented substantial variation in both mutation rates and spectra across primates, the causes of which remain unclear. Here, we review what is currently known about mutation rates in primates, highlight the factors proposed to explain the variation across species, and discuss some implications of these findings on our understanding of the chronology of primate evolution and the process of mutagenesis.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States.
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6
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Marshall CR. Using the Fossil Record to Evaluate Timetree Timescales. Front Genet 2019; 10:1049. [PMID: 31803226 PMCID: PMC6871265 DOI: 10.3389/fgene.2019.01049] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.
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Affiliation(s)
- Charles R. Marshall
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA, United States
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7
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Rasmussen DT, Friscia AR, Gutierrez M, Kappelman J, Miller ER, Muteti S, Reynoso D, Rossie JB, Spell TL, Tabor NJ, Gierlowski-Kordesch E, Jacobs BF, Kyongo B, Macharwas M, Muchemi F. Primitive Old World monkey from the earliest Miocene of Kenya and the evolution of cercopithecoid bilophodonty. Proc Natl Acad Sci U S A 2019; 116:6051-6056. [PMID: 30858323 PMCID: PMC6442627 DOI: 10.1073/pnas.1815423116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Old World monkeys (Cercopithecoidea) are a highly successful primate radiation, with more than 130 living species and the broadest geographic range of any extant group except humans. Although cercopithecoids are highly variable in habitat use, social behavior, and diet, a signature dental feature unites all of its extant members: bilophodonty (bi: two, loph: crest, dont: tooth), or the presence of two cross-lophs on the molars. This feature offers an adaptable Bauplan that, with small changes to its individual components, permits its members to process vastly different kinds of food. Old World monkeys diverged from apes perhaps 30 million years ago (Ma) according to molecular estimates, and the molar lophs are sometimes incompletely developed in fossil species, suggesting a mosaic origin for this key adaptation. However, critical aspects of the group's earliest evolution remain unknown because the cercopithecoid fossil record before ∼18 Ma consists of only two isolated teeth, one from Uganda and one from Tanzania. Here we describe a primitive Old World monkey from Nakwai, Kenya, dated at ∼22 Ma, that offers direct evidence for the initial key steps in the evolution of the cercopithecoid dentition. The simple dentition and absence of bilophodonty in the Nakwai monkey indicate that the initial radiation of Old World monkeys was first characterized by a reorganization of basic molar morphology, and a reliance on cusps rather than lophs suggests frugivorous diets and perhaps hard object feeding. Bilophodonty evolved later, likely in response to the inclusion of leaves in the diet.
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Affiliation(s)
- D Tab Rasmussen
- Department of Anthropology, Washington University, St. Louis, MO 63130-4899
| | - Anthony R Friscia
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095-7246
| | - Mercedes Gutierrez
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455
| | - John Kappelman
- Department of Anthropology, The University of Texas,Austin, TX 78712;
- Department of Geological Sciences, The University of Texas, Austin, TX 78712
| | - Ellen R Miller
- Department of Anthropology, Wake Forest University, Winston Salem, NC 27109-7807
| | - Samuel Muteti
- Palaeontology Section, National Museums of Kenya, 00100 Nairobi, Kenya
| | - Dawn Reynoso
- Department of Geoscience, University of Nevada, Las Vegas, NV 89154-4010
| | - James B Rossie
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794
| | - Terry L Spell
- Department of Geoscience, University of Nevada, Las Vegas, NV 89154-4010
| | - Neil J Tabor
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275-0395
| | | | - Bonnie F Jacobs
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275-0395
| | - Benson Kyongo
- Palaeontology Section, National Museums of Kenya, 00100 Nairobi, Kenya
| | - Mathew Macharwas
- Palaeontology Section, National Museums of Kenya, 00100 Nairobi, Kenya
| | - Francis Muchemi
- Palaeontology Section, National Museums of Kenya, 00100 Nairobi, Kenya
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8
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Kaas JH. The origin and evolution of neocortex: From early mammals to modern humans. PROGRESS IN BRAIN RESEARCH 2019; 250:61-81. [DOI: 10.1016/bs.pbr.2019.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:993-1014. [PMID: 29157065 DOI: 10.1080/24701394.2017.1404041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.
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Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Myreya Pinedo-Castro
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Joseph Mark Shostell
- b Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
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10
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Abstract
Our understanding of the chronology of human evolution relies on the “molecular clock” provided by the steady accumulation of substitutions on an evolutionary lineage. Recent analyses of human pedigrees have called this understanding into question by revealing unexpectedly low germline mutation rates, which imply that substitutions accrue more slowly than previously believed. Translating mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may seem, however. We dissect the steps involved, emphasizing that dating evolutionary events requires not “a mutation rate” but a precise characterization of how mutations accumulate in development in males and females—knowledge that remains elusive.
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Affiliation(s)
- Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Ziyue Gao
- Howard Hughes Medical Institute & Dept. of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
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11
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Scally A. The mutation rate in human evolution and demographic inference. Curr Opin Genet Dev 2016; 41:36-43. [PMID: 27589081 DOI: 10.1016/j.gde.2016.07.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Abstract
The germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5×10-9bp-1year-1 in all human or hominin demographic analyses.
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Affiliation(s)
- Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom.
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12
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Reply to Almécija: A new direction for reconstructing our last common ancestor with chimpanzees. Proc Natl Acad Sci U S A 2016; 113:E945. [PMID: 26862164 DOI: 10.1073/pnas.1525673113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Nowak MG, Reichard UH. Locomotion and Posture in Ancestral Hominoids Prior to the Split of Hylobatids. DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Abstract
CONTEXT The evidence is mounting that reticulate (web-like) evolution has shaped the biological histories of many macroscopic plants and animals, including non-human primates closely related to Homo sapiens, but the implications of this non-hierarchical evolution for anthropological enquiry are not yet fully understood. When they are understood, the result may be a paradigm shift in evolutionary anthropology. OBJECTIVE/METHODS This paper reviews the evidence for reticulated evolution in the non-human primates and human lineage. Then it makes the case for extrapolating this sort of patterning to Homo sapiens and other hominins and explores the implications this would have for research design, method and understandings of evolution in anthropology. RESULTS/CONCLUSION Reticulation was significant in human evolutionary history and continues to influence societies today. Anthropologists and human scientists-whether working on ancient or modern populations-thus need to consider the implications of non-hierarchic evolution, particularly where molecular clocks, mathematical models and simplifying assumptions about evolutionary processes are used. This is not just a problem for palaeoanthropology. The simple fact of different mating systems among modern human groups, for example, may demand that more attention is paid to the potential for complexity in human genetic and cultural histories.
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Affiliation(s)
- Isabelle C Winder
- Department of Archaeology, University of York , the King's Manor, York , United Kingdom and
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15
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Contrasting Phylogenetic and Diversity Patterns in Octodontoid Rodents and a New Definition of the Family Abrocomidae. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9301-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Braga J, Loubes JM, Descouens D, Dumoncel J, Thackeray JF, Kahn JL, de Beer F, Riberon A, Hoffman K, Balaresque P, Gilissen E. Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes' Hearing Evolution. PLoS One 2015; 10:e0127780. [PMID: 26083484 PMCID: PMC4471221 DOI: 10.1371/journal.pone.0127780] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/18/2015] [Indexed: 11/30/2022] Open
Abstract
Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record.
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Affiliation(s)
- J. Braga
- Hominid Evolutionary Biology, AMIS-UMR 5288 CNRS, University of Toulouse (Paul Sabatier), Toulouse, France
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - J-M. Loubes
- Statistics and Probabilities Team, Institute of Mathematics of Toulouse, UMR 5219 CNRS-Université de Toulouse (Paul Sabatier), Toulouse, France
| | - D. Descouens
- Hominid Evolutionary Biology, AMIS-UMR 5288 CNRS, University of Toulouse (Paul Sabatier), Toulouse, France
| | - J. Dumoncel
- Hominid Evolutionary Biology, AMIS-UMR 5288 CNRS, University of Toulouse (Paul Sabatier), Toulouse, France
| | - J. F. Thackeray
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - J-L. Kahn
- Institut d'Anatomie Normale et Pathologique, Faculté de Médecine de Strasbourg, Strasbourg, France
| | - F. de Beer
- South African Nuclear Energy Corporation, Pelindaba, North West Province, South Africa
| | - A. Riberon
- Laboratoire Evolution et Diversité Biologique, UMR 5174 CNRS, University of Toulouse (Paul Sabatier), Toulouse, France
| | - K. Hoffman
- South African Nuclear Energy Corporation, Pelindaba, North West Province, South Africa
| | - P. Balaresque
- Hominid Evolutionary Biology, AMIS-UMR 5288 CNRS, University of Toulouse (Paul Sabatier), Toulouse, France
| | - E. Gilissen
- Royal Museum for Central Africa, Tervuren, Belgium and Laboratory of Histology and Neuropathology, Université libre de Bruxelles, Brussels, Belgium
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Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2014; 75:165-83. [PMID: 24583291 PMCID: PMC4059600 DOI: 10.1016/j.ympev.2014.02.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 01/23/2023]
Abstract
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
| | - Jason A Hodgson
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Andrew S Burrell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States.
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, OR, United States.
| | - Ryan L Raaum
- New York Consortium in Evolutionary Primatology, United States; Department of Anthropology, Lehman College & The Graduate Center, City University of New York, Bronx, NY, United States.
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States.
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18
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Pozzi L, Disotell TR, Masters JC. A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae). BMC Evol Biol 2014; 14:72. [PMID: 24694188 PMCID: PMC4021292 DOI: 10.1186/1471-2148-14-72] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 03/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bushbabies (Galagidae) are among the most morphologically cryptic of all primates and their diversity and relationships are some of the most longstanding problems in primatology. Our knowledge of galagid evolutionary history has been limited by a lack of appropriate molecular data and a paucity of fossils. Most phylogenetic studies have produced conflicting results for many clades, and even the relationships among genera remain uncertain. To clarify galagid evolutionary history, we assembled the largest molecular dataset for galagos to date by sequencing 27 independent loci. We inferred phylogenetic relationships using concatenated maximum-likelihood and Bayesian analyses, and also coalescent-based species tree methods to account for gene tree heterogeneity due to incomplete lineage sorting. RESULTS The genus Euoticus was identified as sister taxon to the rest of the galagids and the genus Galagoides was not recovered as monophyletic, suggesting that a new generic name for the Zanzibar complex is required. Despite the amount of genetic data collected in this study, the monophyly of the family Lorisidae remained poorly supported, probably due to the short internode between the Lorisidae/Galagidae split and the origin of the African and Asian lorisid clades. One major result was the relatively old origin for the most recent common ancestor of all living galagids soon after the Eocene-Oligocene boundary. CONCLUSIONS Using a multilocus approach, our results suggest an early origin for the crown Galagidae, soon after the Eocene-Oligocene boundary, making Euoticus one of the oldest lineages within extant Primates. This result also implies that one - or possibly more - stem radiations diverged in the Late Eocene and persisted for several million years alongside members of the crown group.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, USA
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, USA
| | - Judith C Masters
- African Primate Initiative for Ecology and Speciation, Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
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Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 2014; 9:e85761. [PMID: 24614886 PMCID: PMC3948623 DOI: 10.1371/journal.pone.0085761] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/06/2013] [Indexed: 01/08/2023] Open
Abstract
Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.
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20
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Rodriguez IA, Welsh RM. Possible role of a cell surface carbohydrate in evolution of resistance to viral infections in old world primates. J Virol 2013; 87:8317-26. [PMID: 23740988 PMCID: PMC3719810 DOI: 10.1128/jvi.01118-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/26/2013] [Indexed: 11/20/2022] Open
Abstract
Due to inactivation of the α1,3-galactosyltransferase gene (GGTA1, or the α1,3GT gene) approximately 28 million years ago, the carbohydrate αGal (Galα1,3Galβ1,4GlcNAc) is not expressed on the cells of Old World monkeys and apes (including humans) but is expressed in all other mammals. The proposed selective advantage of this mutation for these primates is the ability to produce anti-Gal antibodies, which may be an effective immune component in neutralizing αGal-expressing pathogens. However, loss of α1,3GT expression may have been advantageous by providing natural resistance against viral pathogens that exploited the α1,3GT pathway or cell surface αGal for infection. Infections of paired cell lines with differential expression of α1,3GT showed that Sindbis viruses (SINV) preferentially replicate in α1,3GT-positive cells, whereas herpes simplex viruses type 1 and type 2 (HSV-1 and HSV-2) preferentially grow in cells lacking α1,3GT. Viral growth and spread correlated with the ability of the different viruses to successfully initiate infection in the presence or absence of α1,3GT expression. GT knockout (KO) suckling mice infected with SINV strains (AR339 and S.A.AR86) experienced significant delay in onset of disease symptoms and mortality compared to wild-type (WT) B6 suckling mice. In contrast, HSV-2-infected GT KO mice had higher viral titers in spleen and liver and exhibited significantly more focal hepatic necrosis than WT B6 mice. This study demonstrates that α1,3GT activity plays a role in the course of infections for certain viruses. Furthermore, this study has implications for the evolution of resistance to viral infections in primates.
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MESH Headings
- Alphavirus Infections/pathology
- Alphavirus Infections/virology
- Animals
- Cell Line
- Cercopithecidae
- Disease Models, Animal
- Disease Resistance
- Evolution, Molecular
- Female
- Galactosyltransferases/genetics
- Galactosyltransferases/metabolism
- Gene Deletion
- Herpes Simplex/pathology
- Herpes Simplex/virology
- Herpesvirus 1, Human/growth & development
- Herpesvirus 1, Human/physiology
- Herpesvirus 2, Human/growth & development
- Herpesvirus 2, Human/physiology
- Humans
- Liver/pathology
- Liver/virology
- Male
- Mice
- Mice, Knockout
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Selection, Genetic
- Sindbis Virus/growth & development
- Sindbis Virus/pathogenicity
- Sindbis Virus/physiology
- Spleen/pathology
- Spleen/virology
- Virus Diseases/immunology
- Virus Internalization
- Virus Physiological Phenomena
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Affiliation(s)
- Idalia A. Rodriguez
- Department of Anthropology, University of Massachusetts at Amherst, Amherst, Massachusetts, USA
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Raymond M. Welsh
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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21
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Van Arsdale AP. A Shifting Theoretical Framework for Biological Anthropology in 2012. AMERICAN ANTHROPOLOGIST 2013. [DOI: 10.1111/aman.12008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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22
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Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes. Nature 2013; 497:611-4. [PMID: 23676680 DOI: 10.1038/nature12161] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/05/2013] [Indexed: 11/08/2022]
Abstract
Apes and Old World monkeys are prominent components of modern African and Asian ecosystems, yet the earliest phases of their evolutionary history have remained largely undocumented. The absence of crown catarrhine fossils older than ∼20 million years (Myr) has stood in stark contrast to molecular divergence estimates of ∼25-30 Myr for the split between Cercopithecoidea (Old World monkeys) and Hominoidea (apes), implying long ghost lineages for both clades. Here we describe the oldest known fossil 'ape', represented by a partial mandible preserving dental features that place it with 'nyanzapithecine' stem hominoids. Additionally, we report the oldest stem member of the Old World monkey clade, represented by a lower third molar. Both specimens were recovered from a precisely dated 25.2-Myr-old stratum in the Rukwa Rift, a segment of the western branch of the East African Rift in Tanzania. These finds extend the fossil record of apes and Old World monkeys well into the Oligocene epoch of Africa, suggesting a possible link between diversification of crown catarrhines and changes in the African landscape brought about by previously unrecognized tectonic activity in the East African rift system.
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23
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24
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Scally A, Durbin R. Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 2012; 13:745-53. [PMID: 22965354 DOI: 10.1038/nrg3295] [Citation(s) in RCA: 308] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is now possible to make direct measurements of the mutation rate in modern humans using next-generation sequencing. These measurements reveal a value that is approximately half of that previously derived from fossil calibration, and this has implications for our understanding of demographic events in human evolution and other aspects of population genetics. Here, we discuss the implications of a lower-than-expected mutation rate in relation to the timescale of human evolution.
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25
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Dimitrov D, Astrin JJ, Huber BA. Pholcid spider molecular systematics revisited, with new insights into the biogeography and the evolution of the group. Cladistics 2012; 29:132-146. [DOI: 10.1111/j.1096-0031.2012.00419.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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26
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Patel BA, Seiffert ER, Boyer DM, Jacobs RL, St Clair EM, Simons EL. New primate first metatarsals from the Paleogene of Egypt and the origin of the anthropoid big toe. J Hum Evol 2012; 63:99-120. [PMID: 22694838 DOI: 10.1016/j.jhevol.2012.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 02/09/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
The specialized grasping feet of primates, and in particular the nature of the hallucal grasping capabilities of living strepsirrhines and tarsiers (i.e., 'prosimians'), have played central roles in the study of primate origins. Prior comparative studies of first metatarsal (Mt1) morphology have documented specialized characters in living prosimians that are indicative of a more abducted hallux, which in turn is often inferred to be related to an increased ability for powerful grasping. These include a well-developed peroneal process and a greater angle of the proximal articular surface relative to the long axis of the diaphysis. Although known Mt1s of fossil prosimians share these characters with living non-anthropoid primates, Mt1 morphology in the earliest crown group anthropoids is not well known. Here we describe two Mt1s from the Fayum Depression of Egypt - one from the latest Eocene (from the ∼34 Ma Quarry L-41), and one from the later early Oligocene (from the ∼29-30 Ma Quarry M) - and compare them with a sample of extant and fossil primate Mt1s. Multivariate analyses of Mt1 shape variables indicate that the Fayum specimens are most similar to those of crown group anthropoids, and likely belong to the stem catarrhines Catopithecus and Aegyptopithecus specifically, based on analyses of size. Also, phylogenetic analyses with 16 newly defined Mt1 characters support the hypotheses that "prosimian"-like Mt1 features evolved along the primate stem lineage, while crown anthropoid Mt1 morphology and function is derived among primates, and likely differed from that of basal stem anthropoids. The derived loss of powerful hallucal grasping as reflected in the Mt1 morphology of crown anthropoids may reflect long-term selection for improved navigation of large-diameter, more horizontal branches at the expense of movement in smaller, more variably inclined branches in the arboreal environment.
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Affiliation(s)
- Biren A Patel
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794-8081, USA.
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27
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Dimitrov D, Lopardo L, Giribet G, Arnedo MA, Alvarez-Padilla F, Hormiga G. Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling. Proc Biol Sci 2012; 279:1341-50. [PMID: 22048955 PMCID: PMC3282380 DOI: 10.1098/rspb.2011.2011] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 10/11/2011] [Indexed: 11/12/2022] Open
Abstract
In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA sequence data and an extensive taxon sample. We present the first dated orb weaver phylogeny. Our results suggest that orb weavers appeared by the Middle Triassic and underwent a rapid diversification during the end of the Triassic and Early Jurassic. By the second half of the Jurassic, most of the extant orb-weaving families and web designs were already present. The processes that may have given origin to this diversification of lineages and web architectures are discussed. A combination of biotic factors, such as key innovations in web design and silk composition, as well as abiotic environmental changes, may have played important roles in the diversification of orb weavers. Our analyses also show that increased taxon sampling density in both ingroups and outgroups greatly improves phylogenetic accuracy even when extensive data are missing. This effect is particularly important when addition of character data improves gene overlap.
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Affiliation(s)
- Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Zoological Museum, University of Copenhagen, Copenhagen, Denmark.
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28
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Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution. Proc Natl Acad Sci U S A 2012; 109:6006-11. [PMID: 22474376 DOI: 10.1073/pnas.1119506109] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A long-standing problem in primate evolution is the discord between paleontological and molecular clock estimates for the time of crown primate origins: the earliest crown primate fossils are ~56 million y (Ma) old, whereas molecular estimates for the haplorhine-strepsirrhine split are often deep in the Late Cretaceous. One explanation for this phenomenon is that crown primates existed in the Cretaceous but that their fossil remains have not yet been found. Here we provide strong evidence that this discordance is better-explained by a convergent molecular rate slowdown in early primate evolution. We show that molecular rates in primates are strongly and inversely related to three life-history correlates: body size (BS), absolute endocranial volume (EV), and relative endocranial volume (REV). Critically, these traits can be reconstructed from fossils, allowing molecular rates to be predicted for extinct primates. To this end, we modeled the evolutionary history of BS, EV, and REV using data from both extinct and extant primates. We show that the primate last common ancestor had a very small BS, EV, and REV. There has been a subsequent convergent increase in BS, EV, and REV, indicating that there has also been a convergent molecular rate slowdown over primate evolution. We generated a unique timescale for primates by predicting molecular rates from the reconstructed phenotypic values for a large phylogeny of living and extinct primates. This analysis suggests that crown primates originated close to the K-Pg boundary and possibly in the Paleocene, largely reconciling the molecular and fossil timescales of primate evolution.
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29
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Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature 2012; 483:169-75. [PMID: 22398555 PMCID: PMC3303130 DOI: 10.1038/nature10842] [Citation(s) in RCA: 460] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 01/10/2012] [Indexed: 12/13/2022]
Abstract
Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.
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Affiliation(s)
- Aylwyn Scally
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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Crisp MD, Cook LG. Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms. THE NEW PHYTOLOGIST 2011; 192:997-1009. [PMID: 21895664 DOI: 10.1111/j.1469-8137.2011.03862.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.
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Affiliation(s)
- Michael D Crisp
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
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Abstract
Natural selection modified the attachment-behavioral system to bond adult mating partners in early members of the genus Homo, thus facilitating increased investment, especially paternal investment, in offspring. Previously existing adaptations that fostered intersexual conflict (e.g., ovulatory adaptations) could have threatened attachment bonds; therefore, the attachment-behavioral system might have evolved the ability to mute or refocus such adaptations for the purpose of strengthening the bond. Two studies offer support for this prediction. Women who were strongly attached to their romantic partner revealed positive associations of fertility with reports of romantic physical intimacy, but these associations were negative among unbonded women. This moderational effect of attachment bond strength was robust beyond dispositional attachment anxiety and avoidance, relationship satisfaction, relationship commitment, and partner physical attractiveness, none of which revealed robust moderational effects. Findings highlight how researchers can use the timeline of hominid evolution (i.e., phylogeny) as a tool to complement functional, adaptationist hypotheses.
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Genomic data reject the hypothesis of a prosimian primate clade. J Hum Evol 2011; 61:295-305. [DOI: 10.1016/j.jhevol.2011.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 01/06/2023]
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Chiou KL, Pozzi L, Lynch Alfaro JW, Di Fiore A. Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences. Mol Phylogenet Evol 2011; 59:736-45. [DOI: 10.1016/j.ympev.2011.03.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 03/17/2011] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
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Pozzi L, Hodgson JA, Burrell AS, Disotell TR. The stem catarrhine Saadanius does not inform the timing of the origin of crown catarrhines. J Hum Evol 2011; 61:209-10. [PMID: 21497373 DOI: 10.1016/j.jhevol.2011.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 11/16/2022]
Affiliation(s)
- Luca Pozzi
- Center for the Study of Human Origins, Department of Anthropology, New York University, USA.
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Kawashima T, Thorington Jr. RW. Comparative Morphological Configuration of the Cardiac Nervous System in Lorises and Galagos (Infraorder Lorisiformes, Strepsirrhini, Primates) with Evolutionary Perspective. Anat Rec (Hoboken) 2011; 294:412-26. [DOI: 10.1002/ar.21334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 11/03/2010] [Indexed: 01/01/2023]
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Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol 2010; 60:16-31. [PMID: 21051775 DOI: 10.1093/sysbio/syq054] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.
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Affiliation(s)
- Richard D Wilkinson
- School of Mathmatical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol Biol Evol 2010; 27:2576-86. [PMID: 20551041 DOI: 10.1093/molbev/msq147] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during the late Jurassic to early Cretaceous (170-120 Ma). This postulated evolutionary scenario agrees well with that based on the paleontological observations.
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Affiliation(s)
- Jun G Inoue
- Department of Biology, University College London, London, United Kingdom
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38
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Heads M. Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00411.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Battistuzzi FU, Filipski A, Hedges SB, Kumar S. Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol 2010; 27:1289-300. [PMID: 20093431 DOI: 10.1093/molbev/msq014] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The rapid expansion of sequence data and the development of statistical approaches that embrace varying evolutionary rates among lineages have encouraged many more investigators to use DNA and protein data to time species divergences. Here, we report results from a systematic evaluation, by means of computer simulation, of the performance of two frequently used relaxed-clock methods for estimating these times and their credibility intervals (CrIs). These relaxed-clock methods allow rates to vary in a phylogeny randomly over lineages (e.g., BEAST software) and in autocorrelated fashion (e.g., MultiDivTime software). We applied these methods for analyzing sequence data sets simulated using naturally derived parameters (evolutionary rates, sequence lengths, and base substitution patterns) and assuming that clock calibrations are known without error. We find that the estimated times are, on average, close to the true times as long as the assumed model of lineage rate changes matches the actual model. The 95% CrIs also contain the true time for >or=95% of the simulated data sets. However, the use of incorrect lineage rate model reduces this frequency to 83%, indicating that the relaxed-clock methods are not robust to the violation of underlying lineage rate model. Because these rate models are rarely known a priori and are difficult to detect empirically, we suggest building composite CrIs using CrIs produced from MultiDivTime and BEAST analysis. These composite CrIs are found to contain the true time for >or=97% data sets. Our analyses also verify the usefulness of the common practice of interpreting the congruence of times inferred from different methods as a reflection of the accuracy of time estimates. Overall, our results show that simple strategies can be used to enhance our ability to estimate times and their CrIs when using the relaxed-clock methods.
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Affiliation(s)
- Fabia U Battistuzzi
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA
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40
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Inoue J, Donoghue PCJ, Yang Z. The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times. Syst Biol 2009; 59:74-89. [DOI: 10.1093/sysbio/syp078] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun Inoue
- Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | | | - Ziheng Yang
- Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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41
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Tsantes C, Steiper ME. Age at first reproduction explains rate variation in the strepsirrhine molecular clock. Proc Natl Acad Sci U S A 2009; 106:18165-70. [PMID: 19841267 PMCID: PMC2775338 DOI: 10.1073/pnas.0906686106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Indexed: 11/18/2022] Open
Abstract
Although the molecular clock hypothesis posits that the rate of molecular change is constant over time, there is evidence that rates vary among lineages. Some of the strongest evidence for variable molecular rates comes from the primates; e.g., the "hominoid slowdown." These rate differences are hypothesized to correlate with certain species attributes, such as generation time and body size. Here, we examine rates of molecular change in the strepsirrhine suborder of primates and test whether body size or age at first reproduction (a proxy for generation time) explains patterns of rate variation better than a null model where the molecular clock is independent of these factors. To examine these models, we analyzed DNA sequences from four pairs of recently diverged strepsirrhine sister taxa to estimate molecular rates by using sign tests, likelihood ratio tests, and regression analyses. Our analysis does not support a model where body weight or age at first reproduction strongly influences rates of molecular evolution across mitochondrial and nuclear sites. Instead, our analysis supports a model where age at first reproduction influences neutral evolution in the nuclear genome. This study supports the generation time hypothesis for rate variation in the nuclear molecular clock. Molecular clock variation due to generation time may help to resolve the discordance between molecular and paleontological estimates for divergence date estimates in primate evolution.
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Affiliation(s)
- C. Tsantes
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY 10065; and
| | - M. E. Steiper
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY 10065; and
- Programs in Anthropology and Biology, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016
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Fabre PH, Rodrigues A, Douzery EJP. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol 2009; 53:808-25. [PMID: 19682589 DOI: 10.1016/j.ympev.2009.08.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/08/2009] [Accepted: 08/03/2009] [Indexed: 11/18/2022]
Abstract
Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.
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Affiliation(s)
- P-H Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France.
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