1
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024; 187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [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: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yuxiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
- Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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3
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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4
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Claramunt S. CladeDate
: Calibration information generator for divergence time estimation. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Santiago Claramunt
- Department of Natural History Royal Ontario Museum Toronto Ontario Canada
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
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5
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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6
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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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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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8
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Dos Reis M. Dating Microbial Evolution with MCMCtree. Methods Mol Biol 2022; 2569:3-22. [PMID: 36083441 DOI: 10.1007/978-1-0716-2691-7_1] [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] [Indexed: 05/24/2023]
Abstract
This protocol explains how to use the program MCMCtree to estimate divergence times in microbial phylogenies. The main advantage of MCMCtree is the implementation of an approximation to the molecular data likelihood that dramatically speeds up computation during Bayesian MCMC sampling of divergence times and evolutionary rates. The approximation allows the analysis of large phylogenies with hundreds of taxa and molecular alignments with thousands or millions of sites. Two examples are used to illustrate Bayesian clock dating with MCMCtree. The first is a phylogeny of (mostly) microbial eukaryotes and prokaryotes encompassing the major groups of life on Earth, and for which fossil information, to calibrate the nodes of the phylogeny, is available. The second is a phylogeny of influenza viruses with known sampling times. An overview of Bayesian MCMC sampling is given as well as practical advice on issues such as construction of the time and rate prior and assessment of convergence of MCMC chains. Strategies for estimating times in microbial phylogenies for which neither fossil information nor sampling times are known are discussed.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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9
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Bobe R, Wood B. Estimating origination times from the early hominin fossil record. Evol Anthropol 2021; 31:92-102. [PMID: 34662482 DOI: 10.1002/evan.21928] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/25/2021] [Accepted: 09/30/2021] [Indexed: 11/09/2022]
Abstract
The age of the earliest recovered fossil evidence of a hominin taxon is all too often equated with that taxon's origination. However, the earliest known fossil record nearly always postdates, sometimes by a substantial period of time, the true origination of a taxon. Here we evaluate the first appearance records of the earliest potential hominins (Sahelanthropus, Ardipithecus, Orrorin), as well as of the genera Australopithecus, Homo, and Paranthropus, to illustrate the considerable uncertainty regarding the actual timing of origin of these taxa. By placing confidence intervals on the first appearance records of early hominin taxa, we can better evaluate patterns of hominin diversity, turnover, and potential correlations with climatic and environmental changes.
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Affiliation(s)
- René Bobe
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford, UK.,Gorongosa National Park, Sofala, Mozambique.,Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Bernard Wood
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia, USA
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10
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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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11
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Brinkworth JF, Valizadegan N. Sepsis and the evolution of human increased sensitivity to lipopolysaccharide. Evol Anthropol 2021; 30:141-157. [PMID: 33689211 DOI: 10.1002/evan.21887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/29/2020] [Accepted: 01/30/2021] [Indexed: 01/03/2023]
Abstract
Among mammals, humans are exquisitely sensitive to lipopolysaccharide (LPS), an environmentally pervasive bacterial cell membrane component. Very small doses of LPS trigger powerful immune responses in humans and can even initiate symptoms of sepsis. Close evolutionary relatives such as African and Asian monkeys require doses that are an order of magnitude higher to do the same. Why humans have evolved such an energetically expensive antimicrobial strategy is a question that biological anthropologists are positioned to help address. Here we compare LPS sensitivity in primate/mammalian models and propose that human high sensitivity to LPS is adaptive, linked to multiple immune tactics against pathogens, and part of multi-faceted anti-microbial strategy that strongly overlaps with that of other mammals. We support a notion that LPS sensitivity in humans has been driven by microorganisms that constitutively live on us, and has been informed by human behavioral changes over our species' evolution (e.g., meat eating, agricultural practices, and smoking).
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Affiliation(s)
- Jessica F Brinkworth
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Animal Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Negin Valizadegan
- Evolutionary Immunology and Genomics Laboratory, Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.,Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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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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13
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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14
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Zardoya R. Quest for the Best Evolutionary Model. J Mol Evol 2020; 89:146-150. [PMID: 33201312 DOI: 10.1007/s00239-020-09971-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
In the early 1980s, DNA sequencing became a routine and the increasing computing power opened the door to reconstruct molecular phylogenies using probabilistic approaches. DNA sequence alignments provided a large number of positions containing phylogenetic information, which could be extracted using explicit statistical models that described the mutation process using appropriate parameters. Consequently, an active quest started for building increasingly improved (more realistic) statistical models of nucleotide substitution. The simplest model assumed that nucleotide frequencies were in equilibrium and one single category of substitutions. Subsequent models allowed either unequal nucleotide frequencies or separate rates for transitions and transversions. The HKY85 model (Hasegawa et al. in J Mol Evol 22:160, 1985) combined elegantly both options into a single model, which became one of the most useful ones and has been the choice in many molecular phylogenetic studies ever since. The use of improved substitution models such as HKY85 allows reconstructing more accurate and reliable phylogenies, which in turn provide robust frameworks for understanding how biological diversity evolved and for performing a wealth of comparative studies in different disciplines such as ecology, biogeography, developmental biology, biochemistry, genomics, epidemiology, and biomedicine.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
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15
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Clarté G, Robert CP, Ryder RJ, Stoehr J. Componentwise approximate Bayesian computation via Gibbs-like steps. Biometrika 2020. [DOI: 10.1093/biomet/asaa090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Summary
Approximate Bayesian computation methods are useful for generative models with intractable likelihoods. These methods are, however, sensitive to the dimension of the parameter space, requiring exponentially increasing resources as this dimension grows. To tackle this difficulty we explore a Gibbs version of the approximate Bayesian computation approach that runs component-wise approximate Bayesian computation steps aimed at the corresponding conditional posterior distributions, and based on summary statistics of reduced dimensions. While lacking the standard justifications for the Gibbs sampler, the resulting Markov chain is shown to converge in distribution under some partial independence conditions. The associated stationary distribution can further be shown to be close to the true posterior distribution, and some hierarchical versions of the proposed mechanism enjoy a closed-form limiting distribution. Experiments also demonstrate the gain in efficiency brought by the Gibbs version over the standard solution.
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Affiliation(s)
- Grégoire Clarté
- CEREMADE, Université Paris-Dauphine, Place du Maréchal de Lattre de Tassigny, 75775 Paris, Cedex 16, France
| | - Christian P Robert
- CEREMADE, Université Paris-Dauphine, Place du Maréchal de Lattre de Tassigny, 75775 Paris, Cedex 16, France
| | - Robin J Ryder
- CEREMADE, Université Paris-Dauphine, Place du Maréchal de Lattre de Tassigny, 75775 Paris, Cedex 16, France
| | - Julien Stoehr
- CEREMADE, Université Paris-Dauphine, Place du Maréchal de Lattre de Tassigny, 75775 Paris, Cedex 16, France
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16
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Locke EM, Benefit BR, Kimock CM, Miller ER, Nengo I. New dentognathic fossils of Noropithecus bulukensis (Primates, Victoriapithecidae) from the late Early Miocene of Buluk, Kenya. J Hum Evol 2020; 148:102886. [PMID: 33031954 DOI: 10.1016/j.jhevol.2020.102886] [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: 01/28/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
The late Early Miocene site of Buluk, Kenya, has yielded fossil remains of several catarrhine primates, including 16 dentognathic specimens of the stem cercopithecoid Noropithecus bulukensis. With the exception of the large sample of Victoriapithecus macinnesi from the middle Miocene of Maboko Island, Kenya, the majority of stem cercopithecoid taxa are represented by small sample sizes. We describe and analyze 91 new cercopithecoid fossils collected from Buluk between 2004 and 2018, including several previously undescribed tooth positions for N. bulukensis, and provide the first evaluation of dental metric and morphological variation in this sample. The results show that the expanded Buluk sample exhibits high levels of dental variation in the postcanine tooth row, similar to V. macinnesi at Maboko, but this variation is consistent with a single-species hypothesis. Subtle differences in the shape of the I1, breadth of the C1 and P3, relative breadth of M1, upper and lower molar distal shelf lengths, the degree of M2 basal flare, and a less-developed lower molar distal lophid differentiate the dentition of N. bulukensis from V. macinnesi. Although differences exist between the N. bulukensis and V. macinnesi dental samples, the high degree of variation within each sample complicates the identification of many individual specimens. New partial maxillae and mandibles allow reassessment of previously described diagnostic differences between N. bulukensis and V. macinnesi, negating upper molar arcade shape as a diagnostic feature and confirming the existence of differences in mandibular symphyseal morphology. Overall, new fossils from Buluk provide new evidence of the dentognathic anatomy of a medium-sized cercopithecoid that coexisted with a diverse group of noncercopithecoid catarrhines at the end of the early Miocene.
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Affiliation(s)
- Ellis M Locke
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85282, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85282, USA.
| | - Brenda R Benefit
- Department of Anthropology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Clare M Kimock
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, NY, 10003, USA; New York Consortium in Evolutionary Primatology, New York, NY, 10003, USA
| | - Ellen R Miller
- Department of Anthropology, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Isaiah Nengo
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY, 11794, USA
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17
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Warne DJ, Baker RE, Simpson MJ. Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art. J R Soc Interface 2020; 16:20180943. [PMID: 30958205 DOI: 10.1098/rsif.2018.0943] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealizations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time-course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with Matlab® implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community.
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Affiliation(s)
- David J Warne
- 1 School of Mathematical Sciences, Queensland University of Technology , Brisbane, Queensland 4001 , Australia
| | - Ruth E Baker
- 2 Mathematical Institute, University of Oxford , Oxford OX2 6GG , UK
| | - Matthew J Simpson
- 1 School of Mathematical Sciences, Queensland University of Technology , Brisbane, Queensland 4001 , Australia
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18
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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19
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White S, Soligo C, Pope M, Hillson S. Taxonomic variation in the supraorbital region of catarrhine primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171:198-218. [PMID: 31762014 DOI: 10.1002/ajpa.23975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/07/2022]
Abstract
OBJECTIVES This study aimed to test the taxonomic utility of the catarrhine supraorbital region using 3D geometric morphometrics, with the aim of establishing its potential use in elucidating the position of more debated hominin groups. MATERIALS AND METHODS 230 3D coordinates were used to record the supraorbital morphology of two datasets: one containing 460 non-hominin catarrhine primates from species and subspecies of Gorilla, Pan, Papio, and Macaca; and the other containing 55 Pleistocene hominins from Homo, Australopithecus, and Paranthropus. Principal component analyses in tangent, form, and allometry-free shape space were used to assess differentiation of taxa, with biological distinctiveness of taxa being established using step-wise discriminant analysis with subsampling. RESULTS Results indicated that the recorded supraorbital morphology could be used to separate non-hominin catarrhine primate genera, species, and subspecies, although accuracy was found to decrease with decreasing Linnaean rank. In addition, analyses in tangent space were found to produce the highest accuracy when classifying primates of known taxonomy. Biological distinctiveness of the middle and later Homo species was comparable to or higher than that of the non-hominin primates, and relatively lower for the earlier groups of Homo. DISCUSSION This study indicates that the supraorbital region preserves taxonomic information that can be used to delineate between closely related groups, both within hominins and wider catarrhine primates. Therefore, this region may be used to provide insight when assessing the taxonomic affiliation of disputed hominin specimens.
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Affiliation(s)
- Suzanna White
- Department of Anthropology, University College London, London, UK
| | | | - Matt Pope
- Institute of Archaeology, University College London, London, UK
| | - Simon Hillson
- Institute of Archaeology, University College London, London, UK
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20
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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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21
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Bryant KL, Glasser MF, Li L, Jae-Cheol Bae J, Jacquez NJ, Alarcón L, Fields A, Preuss TM. Organization of extrastriate and temporal cortex in chimpanzees compared to humans and macaques. Cortex 2019; 118:223-243. [PMID: 30910223 PMCID: PMC6697630 DOI: 10.1016/j.cortex.2019.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/31/2018] [Accepted: 02/13/2019] [Indexed: 01/11/2023]
Abstract
There is evidence for enlargement of association cortex in humans compared to other primate species. Expansion of temporal association cortex appears to have displaced extrastriate cortex posteriorly and inferiorly in humans compared to macaques. However, the details of the organization of these recently expanded areas are still being uncovered. Here, we used diffusion tractography to examine the organization of extrastriate and temporal association cortex in chimpanzees, humans, and macaques. Our goal was to characterize the organization of visual and auditory association areas with respect to their corresponding primary areas (primary visual cortex and auditory core) in humans and chimpanzees. We report three results: (1) Humans, chimpanzees, and macaques show expected retinotopic organization of primary visual cortex (V1) connectivity to V2 and to areas immediately anterior to V2; (2) In contrast to macaques, chimpanzee and human V1 shows apparent connectivity with lateral, inferior, and anterior temporal regions, beyond the retinotopically organized extrastriate areas; (3) Also in contrast to macaques, chimpanzee and human auditory core shows apparent connectivity with temporal association areas, with some important differences between humans and chimpanzees. Diffusion tractography reconstructs diffusion patterns that reflect white matter organization, but does not definitively represent direct anatomical connectivity. Therefore, it is important to recognize that our findings are suggestive of species differences in long-distance white matter organization rather than demonstrations of direct connections. Our data support the conclusion that expansion of temporal association cortex, and the resulting posterior displacement of extrastriate cortex, occurred in the human lineage after its separation from the chimpanzee lineage. It is possible, however, that some expansion of the temporal lobe occurred prior to the separation of humans and chimpanzees, reflected in the reorganization of long white matter tracts in the temporal lobe that connect occipital areas to the fusiform gyrus, middle temporal gyrus, and anterior temporal lobe.
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Affiliation(s)
- Katherine L Bryant
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Matthew F Glasser
- Departments of Radiology and Neuroscience, Washington University Medical School, St. Louis, MO, USA
| | - Longchuan Li
- Marcus Autism Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Jason Jae-Cheol Bae
- Neuroscience and Behavioral Biology, Emory University, Atlanta, GA, USA; College of Medicine, American University of Antigua, USA
| | - Nadine J Jacquez
- Neuroscience and Behavioral Biology, Emory University, Atlanta, GA, USA
| | - Laura Alarcón
- Neuroscience and Behavioral Biology, Emory University, Atlanta, GA, USA
| | - Archie Fields
- Department of Philosophy, University of Calgary, Calgary, Alberta, Canada
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Center for Translational Social Neuroscience, Emory University, Atlanta, GA, USA; Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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22
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Lin MK, Takahashi YS, Huo BX, Hanada M, Nagashima J, Hata J, Tolpygo AS, Ram K, Lee BC, Miller MI, Rosa MGP, Sasaki E, Iriki A, Okano H, Mitra P. A high-throughput neurohistological pipeline for brain-wide mesoscale connectivity mapping of the common marmoset. eLife 2019; 8:e40042. [PMID: 30720427 PMCID: PMC6384052 DOI: 10.7554/elife.40042] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/04/2019] [Indexed: 11/13/2022] Open
Abstract
Understanding the connectivity architecture of entire vertebrate brains is a fundamental but difficult task. Here we present an integrated neuro-histological pipeline as well as a grid-based tracer injection strategy for systematic mesoscale connectivity mapping in the common marmoset (Callithrix jacchus). Individual brains are sectioned into ~1700 20 µm sections using the tape transfer technique, permitting high quality 3D reconstruction of a series of histochemical stains (Nissl, myelin) interleaved with tracer labeled sections. Systematic in-vivo MRI of the individual animals facilitates injection placement into reference-atlas defined anatomical compartments. Further, by combining the resulting 3D volumes, containing informative cytoarchitectonic markers, with in-vivo and ex-vivo MRI, and using an integrated computational pipeline, we are able to accurately map individual brains into a common reference atlas despite the significant individual variation. This approach will facilitate the systematic assembly of a mesoscale connectivity matrix together with unprecedented 3D reconstructions of brain-wide projection patterns in a primate brain.
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Affiliation(s)
- Meng Kuan Lin
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
| | | | - Bing-Xing Huo
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
| | - Mitsutoshi Hanada
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
| | - Jaimi Nagashima
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
| | - Junichi Hata
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
| | | | | | - Brian C Lee
- Center for Imaging ScienceJohns Hopkins UniversityMarylandUnited States
| | - Michael I Miller
- Center for Imaging ScienceJohns Hopkins UniversityMarylandUnited States
| | - Marcello GP Rosa
- Department of Physiology and Biomedicine, Discovery InstituteMonash UniversityMelbourneAustralia
- Australian Research Council Centre of Excellence for Integrative Brain FunctionClaytonAustralia
| | - Erika Sasaki
- Central Institute for Experimental AnimalsKawasakiJapan
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive DevelopmentRIKEN Center for Brain ScienceWakoJapan
| | - Hideyuki Okano
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
- Department of PhysiologyKeio University School of MedicineTokyoJapan
| | - Partha Mitra
- Laboratory for Marmoset Neural ArchitectureRIKEN Center for Brain ScienceWakoJapan
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
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23
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Pârvulescu L, Pérez‐Moreno JL, Panaiotu C, Drăguț L, Schrimpf A, Popovici I, Zaharia C, Weiperth A, Gál B, Schubart CD, Bracken‐Grissom H. A journey on plate tectonics sheds light on European crayfish phylogeography. Ecol Evol 2019; 9:1957-1971. [PMID: 30847085 PMCID: PMC6392496 DOI: 10.1002/ece3.4888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 12/08/2018] [Accepted: 12/14/2018] [Indexed: 12/03/2022] Open
Abstract
Crayfish can be used as model organisms in phylogeographic and divergence time studies if reliable calibrations are available. This study presents a comprehensive investigation into the phylogeography of the European stone crayfish (Austropotamobius torrentium) and includes samples from previously unstudied sites. Two mitochondrial markers were used to reveal evolutionary relationships among haplogroups throughout the species' distributional range and to estimate the divergence time by employing both substitution rates and geological calibration methods. Our haplotype network reconstruction and phylogenetic analyses revealed the existence of a previously unknown haplogroup distributed in Romania's Apuseni Mountains. This haplogroup is closely related to others that are endemic in the Dinarides, despite their vast geographical separation (~600 km). The separation is best explained by the well-dated tectonic displacement of the Tisza-Dacia microplate, which started in the Miocene (~16 Ma) and possibly carried part of the A. torrentium population to the current location of the Apuseni Mountains. This population may thus have been isolated from the Dinarides for a period of ca. 11 m.y. by marine and lacustrine phases of the Pannonian Basin. The inclusion of this geological event as a calibration point in divergence time analyses challenges currently accepted crayfish evolutionary time frames for the region, constraining the evolution of this area's crayfish to a much earlier date. We discuss why molecular clock calibrations previously employed to date European crayfish species divergences should therefore be reconsidered.
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Affiliation(s)
- Lucian Pârvulescu
- Department of Biology‐Chemistry, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
| | - Jorge L. Pérez‐Moreno
- Department of BiologyFlorida International University – Biscayne Bay CampusNorth MiamiFlorida
| | - Cristian Panaiotu
- Paleomagnetic Laboratory, Faculty of PhysicsUniversity of BucharestMagureleRomania
| | - Lucian Drăguț
- Department of Geography, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
| | - Anne Schrimpf
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Ioana‐Diana Popovici
- Department of Biology‐Chemistry, Faculty of Chemistry, Biology, GeographyWest University of TimisoaraTimisoaraRomania
- Institute for Environmental SciencesUniversity Koblenz‐LandauLandauGermany
| | - Claudia Zaharia
- Department of Mathematics, Faculty of Mathematics and Computer ScienceWest University of TimisoaraTimisoaraRomania
| | - András Weiperth
- MTA Centre for Ecological Research, Danube Research InstituteBudapestHungary
| | - Blanka Gál
- MTA Centre for Ecological Research, Danube Research InstituteBudapestHungary
- Doctoral School of Environmental SciencesEötvös Loránd UniversityBudapestHungary
| | - Christoph D. Schubart
- Department of Zoology and Evolutionary BiologyUniversity of RegensburgRegensburgGermany
| | - Heather Bracken‐Grissom
- Department of BiologyFlorida International University – Biscayne Bay CampusNorth MiamiFlorida
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24
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Abstract
Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation in the branches of a phylogenetic tree and the use of flexible fossil calibration densities to describe the uncertainty in node ages. The advent of next-generation sequencing technologies has led to a flood of genome-scale datasets for organisms belonging to all domains in the tree of life. Thus, a new era has begun where dating the tree of life using genome-scale data is now within reach. In this protocol, we explain how to use the computer program MCMCTree to perform Bayesian inference of divergence times using genome-scale datasets. We use a ten-species primate phylogeny, with a molecular alignment of over three million base pairs, as an exemplar on how to carry out the analysis. We pay particular attention to how to set up the analysis and the priors and how to diagnose the MCMC algorithm used to obtain the posterior estimates of divergence times and evolutionary rates.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK.
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25
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Silvestro D, Tejedor MF, Serrano-Serrano ML, Loiseau O, Rossier V, Rolland J, Zizka A, Höhna S, Antonelli A, Salamin N. Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors. Syst Biol 2018; 68:78-92. [PMID: 29931325 PMCID: PMC6292484 DOI: 10.1093/sysbio/syy046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors contributed equally to this work
| | - Marcelo F Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Instituto Patagónico de Geología y Paleontología (CCT CONICET-CENPAT), Boulevard Almirante Brown 2915, 9120 Puerto Madryn, Chubut, Argentina.,Facultad de Ciencias Naturales, Sede Trelew, Universidad Nacional de la Patagonia 'San Juan Bosco', 9100 Trelew, Chubut, Argentina.,These authors contributed equally to this work
| | | | - Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Zoology, University of British Columbia, 2212 Main Mall, Vancouver, BC Canada
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Munich, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Gothenburg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.,These authors are severs as a co-last authorship
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors are severs as a co-last authorship
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26
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Guindon S. Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a "Doubly Intractable" Problem. Syst Biol 2018; 67:651-661. [PMID: 29385558 DOI: 10.1093/sysbio/syy003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
This study introduces a new Bayesian technique for molecular dating that explicitly accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from the analysis of fossil data. The proposed approach thus defines an adequate framework for incorporating expert knowledge and/or prior information about the way fossils were collected in the inference of node ages. Although it belongs to the class of "node-dating" approaches, this method shares interesting properties with "tip-dating" techniques. Yet, it alleviates some of the computational and modeling difficulties that hamper tip-dating approaches. The influence of fossil data on the probabilistic distribution of trees is the crux of the matter considered here. More specifically, among all the phylogenies that a tree model (e.g., the birth-death process) generates, only a fraction of them "agree" with the fossil data. Bayesian inference under the new model requires taking this fraction into account. However, evaluating this quantity is difficult in practice. A generic solution to this issue is presented here. The proposed approach relies on a recent statistical technique, the so-called exchange algorithm, dedicated to drawing samples from "doubly intractable" distributions. A small example illustrates the problem of interest and the impact of uncertainty in the placement of calibration constraints in the phylogeny given fossil data. An analysis of land plant sequences and multiple fossils further highlights the pertinence of the proposed approach.
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS, Université de Montpellier, Montpellier, France
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27
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Reis MD, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD. Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Syst Biol 2018; 67:594-615. [PMID: 29342307 PMCID: PMC6005039 DOI: 10.1093/sysbio/syy001] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 12/26/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gregg F Gunnell
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
| | - Jose Barba-Montoya
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Alex Wilkins
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
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28
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Hlusko LJ. Recent insights into the evolution of quantitative traits in non-human primates. Curr Opin Genet Dev 2018; 53:15-20. [PMID: 29913352 DOI: 10.1016/j.gde.2018.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/25/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
The past few years of genetic research on primate quantitative trait variation have been notable in the diversity of phenotypes explored, ranging from classic skeletal measurements to behavior, through to levels of gene expression, and with observations from both captive and wild populations. These studies demonstrate the importance of captive pedigreed breeding colonies, populations that can be matched to their wild counterparts to enable comparison of genetic architectures. Non-human primate genotype:phenotype maps are essential for placing human variation within an evolutionary framework as well as for gaining insight to human biology. While the demographic history of most primates has been fairly stable since the Late Pleistocene, humans experienced a dramatic population expansion that increased the number of rare, mildly deleterious mutations. These rare genetic variants complicate the genotype:phenotype association because they account for a disproportionate amount of the genetic variance and are harder to detect. The similar physiologies of our closest living relatives may prove to be key for overcoming the hurdles posed by humans' peculiar demographic explosion.
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Affiliation(s)
- Leslea J Hlusko
- Human Evolution Research Center, Department of Integrative Biology, University of California Berkeley, 3040 Valley Life Science Bldg, MC-3140, Berkeley, CA 94720, USA.
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29
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Frias L, Stark DJ, Lynn MS, Nathan SK, Goossens B, Okamoto M, MacIntosh AJJ. Lurking in the dark: Cryptic Strongyloides in a Bornean slow loris. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:141-146. [PMID: 29988792 PMCID: PMC6031959 DOI: 10.1016/j.ijppaw.2018.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 01/15/2023]
Abstract
Within host communities, related species are more likely to share common parasitic agents, and as a result, morphological similarities have led researchers to conclude that parasites infecting closely related hosts within a community represent a single species. However, genetic diversity within parasite genera and host range remain poorly investigated in most systems. Strongyloides is a genus of soil-transmitted nematode that has been reported from several primate species in Africa and Asia, and has been estimated to infect hundreds of millions of people worldwide, although no precise estimates are available. Here we describe a case of infection with a cryptic species of Strongyloides in a Bornean (Philippine) slow loris (Nycticebus menagensis) living within a diverse community of several primate species in the Lower Kinabatangan Wildlife Sanctuary, Malaysian Borneo. Fresh fecal samples were collected from five primate species and nematode larvae cultured from these samples were selected for phylogenetic analyses. Sequences obtained for most larvae were identified as S. fuelleborni, grouping into three different clusters and showing no aggregation within specific hosts or geographic location. In contrast, a set of parasite sequences obtained from a slow loris clustered closely with S. stercoralis into a different group, being genetically distinct to sequences reported from other primate hosts, humans included. Our results suggest that although S. fuelleborni infects all haplorrhines sampled in this primate community, a different species might be infecting the slow loris, the only strepsirrhine in Borneo and one of the least studied primates in the region. Although more data are needed to support this conclusion, we propose that Strongyloides species in primates might be more diverse than previously thought, with potential implications for ecological and evolutionary host-parasite associations, as well as epidemiological dynamics.
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Affiliation(s)
- Liesbeth Frias
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Danica J Stark
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia
| | - Milena Salgado Lynn
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia.,Wildlife Health, Genetic and Forensic Laboratory, Kota Kinabalu, Sabah, Malaysia.,Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | | | - Benoit Goossens
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Danau Girang Field Centre, Lower Kinabatangan Wildlife Sanctuary, Sabah, Malaysia.,Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia.,Sustainable Places Research Institute, Cardiff University, Cardiff, UK
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30
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Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol Biol 2018; 18:23. [PMID: 29463217 PMCID: PMC5819086 DOI: 10.1186/s12862-018-1141-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.
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Affiliation(s)
- F Welker
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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31
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Matschiner M, Musilová Z, Barth JMI, Starostová Z, Salzburger W, Steel M, Bouckaert R. Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes. Syst Biol 2018; 66:3-22. [PMID: 28173588 DOI: 10.1093/sysbio/syw076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/21/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
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Affiliation(s)
- Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Zuzana Musilová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Julia M I Barth
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Mike Steel
- Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Remco Bouckaert
- Department of Computer Science, University of Auckland, Auckland, New Zealand.,Computational Evolution Group, University of Auckland, Auckland, New Zealand
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32
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Warnock RCM, Yang Z, Donoghue PCJ. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proc Biol Sci 2018. [PMID: 28637852 PMCID: PMC5489717 DOI: 10.1098/rspb.2017.0227] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.
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Affiliation(s)
- Rachel C M Warnock
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK .,Department of Paleobiology, National Museum of Natural History, The Smithsonian Institution, Washington, DC 20560, USA.,Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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33
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Sarmiento EE. Fossil genera and wastebasket taxa in the human lineage: in support of Tattersall. Evol Anthropol 2017; 26:267-269. [PMID: 29265655 DOI: 10.1002/evan.21556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/09/2022]
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34
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Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW. Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 2017; 93:1165-1191. [DOI: 10.1111/brv.12390] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Lindell Bromham
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne VIC 3010 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Xia Hua
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Andrew M. Ritchie
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - David A. Duchêne
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
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Dos Reis M. Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0128. [PMID: 27325826 DOI: 10.1098/rstb.2015.0128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/12/2022] Open
Abstract
Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK Department of Genetics, Evolution and Environment, University College London, Gower Street, London W1C 6BT, UK
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Rannala B. Conceptual issues in Bayesian divergence time estimation. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0134. [PMID: 27325831 DOI: 10.1098/rstb.2015.0134] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2016] [Indexed: 11/12/2022] Open
Abstract
Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
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Yang Z, Donoghue PCJ. Dating species divergences using rocks and clocks. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0126. [PMID: 27325825 DOI: 10.1098/rstb.2015.0126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Novo NM, Tejedor MF, Pérez ME, Krause JM. New primate locality from the early Miocene of Patagonia, Argentina. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:861-867. [PMID: 28895134 DOI: 10.1002/ajpa.23309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/19/2017] [Accepted: 08/23/2017] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The purpose of this work is to present a new primate locality with evidence that increases the knowledge on the radiation of the extinct platyrrhine primates. MATERIALS AND METHODS We studied the new specimen and compared it to specimens identified as Mazzonicebus almendrae. RESULTS The new first and second molars were comparable to Mazzonicebus almendrae in all morphological details, allowing us to allocate the new specimen to M. almendrae and add comments on morphological variation in this species regarding the orientation of the labial cristae and development of the anterolingual cingulum. This new maxilla also present the first known M3 for the species. DISCUSSION The new specimen increases our knowledge of the extinct platyrrhines from Patagonia. Their age and geographical distribution ranges from early to middle Miocene in an area between 40° to 47° of southern latitude.
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Affiliation(s)
- Nelson M Novo
- Instituto Patagónico de Geología y Paleontología (IPGP, CCT CONICET-CENPAT), Boulevard Brown 2915, U91200, Puerto Madryn, Argentina.,Facultad de Ciencias Naturales, Sede Puerto Madryn. Universidad Nacional de la Patagonia "San Juan Bosco", Puerto Madryn, Argentina
| | - Marcelo F Tejedor
- Instituto Patagónico de Geología y Paleontología (IPGP, CCT CONICET-CENPAT), Boulevard Brown 2915, U91200, Puerto Madryn, Argentina.,Facultad de Ciencias Naturales, Sede Trelew. Universidad Nacional de la Patagonia "San Juan Bosco", Trelew, Argentina.,Gothenburg Global Biodiversity Centre, Box 461, 405-30 Göteborg, Sweden
| | - María E Pérez
- CONICET, Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, U9100GYO, Chubut, Argentina.,Research Associate, Field Museum of Natural History, Chicago, IL, USA
| | - J Marcelo Krause
- CONICET, Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, U9100GYO, Chubut, Argentina.,Departamento de Geología, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial 1 s/n, Comodoro Rivadavia, 9000, Chubut, Argentina
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Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol Phylogenet Evol 2017; 114:386-400. [PMID: 28709986 PMCID: PMC5546266 DOI: 10.1016/j.ympev.2017.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/16/2017] [Accepted: 07/09/2017] [Indexed: 11/30/2022]
Abstract
Fossil calibrations are the utmost source of information in molecular clock dating. The quality of calibrations has a major impact on divergence time estimates. In general, truncation has a great impact on calibrations. The different strategies for generating the effective prior also had considerable impact. It is important to inspect the joint time prior used by the dating program before any Bayesian dating analysis.
Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis.
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Bjarnason A, Soligo C, Elton S. Phylogeny, phylogenetic inference, and cranial evolution in pitheciids andAotus. Am J Primatol 2016; 79:1-11. [DOI: 10.1002/ajp.22621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Sarah Elton
- Department of Anthropology; Durham University; Durham DH1 3LE
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Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. Evolution and demography of the great apes. Curr Opin Genet Dev 2016; 41:124-129. [PMID: 27716526 DOI: 10.1016/j.gde.2016.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/27/2023]
Abstract
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Alexander Nater
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maja P Greminger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
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Nova Delgado M, Galbany J, Pérez-Pérez A. Molar shape variability in platyrrhine primates. J Hum Evol 2016; 99:79-92. [PMID: 27650581 DOI: 10.1016/j.jhevol.2016.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/18/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022]
Abstract
Recent phylogenetic analyses suggest that platyrrhines constitute a monophyletic group represented by three families: Cebidae, Atelidae, and Pitheciidae. Morphological variability between and within these three families, however, is widely discussed and debated. The aim of this study was to assess molar shape variability in platyrrhines, to explore patterns of interspecific variation among extant species, and to evaluate how molar shape can be used as a taxonomic indicator. The analyses were conducted using standard multivariate analyses of geometric morphometric data from 802 platyrrhine lower molars. The results indicated that the interspecific variation exhibited a highly homoplastic pattern related to functional adaptation of some taxa. However, phylogeny was also an important factor in shaping molar morphological traits, given that some phenotypic similarities were consistent with current phylogenetic positions. Our results show that the phylogenetic and functional signals of lower molar shape vary depending on the taxa and the tooth considered. Based on molar shape, Aotus showed closer similarities to Callicebus, as well as to some Cebidae and Ateles-Lagothrix, due to convergent evolutionary trends caused by similar dietary habits, or due to fast-evolving branches in the Aotus lineage, somewhat similar to the shape of Callicebus and Cebidae.
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Affiliation(s)
- Mónica Nova Delgado
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Jordi Galbany
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, 800 22nd Street NW, Ste 6000, Washington, D.C. 20052, USA
| | - Alejandro Pérez-Pérez
- Secció de Zoologia i Antropologia Biològica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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Abstract
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years, and the human and gorilla divergence time is 15.1 million years.
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De Baets K, Antonelli A, Donoghue PCJ. Tectonic blocks and molecular clocks. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160098. [PMID: 27325840 PMCID: PMC4920344 DOI: 10.1098/rstb.2016.0098] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2016] [Indexed: 12/03/2022] Open
Abstract
Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Kenneth De Baets
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK GeoZentrum Nordbayern, Fachgruppe PaläoUmwelt, Friedrich-Alexander-Universität Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Göteborg, Sweden
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Donoghue PCJ, Yang Z. The evolution of methods for establishing evolutionary timescales. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160020. [PMID: 27325838 PMCID: PMC4920342 DOI: 10.1098/rstb.2016.0020] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2016] [Indexed: 11/12/2022] Open
Abstract
The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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Marivaux L, Adnet S, Altamirano-Sierra AJ, Boivin M, Pujos F, Ramdarshan A, Salas-Gismondi R, Tejada-Lara JV, Antoine PO. Neotropics provide insights into the emergence of New World monkeys: New dental evidence from the late Oligocene of Peruvian Amazonia. J Hum Evol 2016; 97:159-75. [PMID: 27457552 DOI: 10.1016/j.jhevol.2016.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
Recent field efforts in Peruvian Amazonia (Contamana area, Loreto Department) have resulted in the discovery of a late Oligocene (ca. 26.5 Ma; Chambira Formation) fossil primate-bearing locality (CTA-61). In this paper, we analyze the primate material consisting of two isolated upper molars, the peculiar morphology of which allows us to describe a new medium-sized platyrrhine monkey: Canaanimico amazonensis gen. et sp. nov. In addition to the recent discovery of Perupithecus ucayaliensis, a primitive anthropoid taxon of African affinities from the alleged latest Eocene Santa Rosa locality (Peruvian Amazonia), the discovery of Canaanimico adds to the evidence that primates were well-established in the Amazonian Basin during the Paleogene. Our phylogenetic results based on dental evidence show that none of the early Miocene Patagonian taxa (Homunculus, Carlocebus, Soriacebus, Mazzonicebus, Dolichocebus, Tremacebus, and Chilecebus), the late Oligocene Bolivian Branisella, or the Peruvian Canaanimico, is nested within a crown platyrrhine clade. All these early taxa are closely related and considered here as stem Platyrrhini. Canaanimico is nested within the Patagonian Soriacebinae, and closely related to Soriacebus, thereby extending back the soriacebine lineage to 26.5 Ma. Given the limited dental evidence, it is difficult to assess if Canaanimico was engaged in a form of pitheciine-like seed predation as is observed in Soriacebus and Mazzonicebus, but dental microwear patterns recorded on one upper molar indicate that Canaanimico was possibly a fruit and hard-object eater. If Panamacebus, a recently discovered stem cebine from the early Miocene of Panama, indicates that the crown platyrrhine radiation was already well underway by the earliest Miocene, Canaanimico indicates in turn that the "homunculid" radiation (as a part of the stem radiation) was well underway by the late Oligocene. These new data suggest that the stem radiation likely occurred in the Neotropics during the Oligocene, and that several stem lineages independently reached Patagonia during the early Miocene. Finally, we are still faced with a "layered" pattern of platyrrhine evolution, but modified in terms of timing of cladogeneses. If the crown platyrrhine radiation occurred in the Neotropics around the Oligocene-Miocene transition (or at least during the earliest Miocene), it was apparently concomitant with the diversification of the latest stem forms in Patagonia.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France.
| | - Sylvain Adnet
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Ali J Altamirano-Sierra
- Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru
| | - Myriam Boivin
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales (IANIGLA), CCT-CONICET-Mendoza, Av. Ruiz Leal s/n, Parque Gral. San Martín, 5500 Mendoza, Argentina
| | - Anusha Ramdarshan
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France
| | - Rodolfo Salas-Gismondi
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France; Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru
| | - Julia V Tejada-Lara
- Departamento de Paleontología de Vertebrados, Museo de Historia Natural - Universidad Nacional Mayor San Marcos (MUSM), Av. Arenales 1256, Lima 11, Peru; Columbia University in the City of New York and Division of Vertebrate Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France.
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Nova Delgado M, Galbany J, Pérez-Pérez A. Morphometric variation of extant platyrrhine molars: taxonomic implications for fossil platyrrhines. PeerJ 2016; 4:e1967. [PMID: 27190704 PMCID: PMC4867715 DOI: 10.7717/peerj.1967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/04/2016] [Indexed: 12/25/2022] Open
Abstract
The phylogenetic position of many fossil platyrrhines with respect to extant ones is not yet clear. Two main hypotheses have been proposed: the layered or successive radiations hypothesis suggests that Patagonian fossils are Middle Miocene stem platyrrhines lacking modern descendants, whereas the long lineage hypothesis argues for an evolutionary continuity of all fossil platyrrhines with the extant ones. Our geometric morphometric analysis of a 15 landmark-based configuration of platyrrhines' first and second lower molars suggest that morphological stasis may explain the reduced molar shape variation observed. Platyrrhine lower molar shape might be a primitive retention of the ancestral state affected by strong ecological constraints throughout the radiation of the main platyrrhine families. The Patagonian fossil specimens showed two distinct morphological patterns of lower molars, Callicebus-like and Saguinus-like, which might be the precursors of the extant forms, whereas the Middle Miocene specimens, though showing morphological resemblances with the Patagonian fossils, also displayed new, derived molar patterns, Alouatta-like and Pitheciinae-like, thereby suggesting that despite the overall morphological stasis of molars, phenotypic diversification of molar shape was already settled during the Middle Miocene.
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Affiliation(s)
- Mónica Nova Delgado
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona , Barcelona , Spain
| | - Jordi Galbany
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona, Barcelona, Spain; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, Washington DC, United States of America
| | - Alejandro Pérez-Pérez
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Zoology and Physical Anthropology Section, Universitat de Barcelona , Barcelona , Spain
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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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Soligo C, Smaers JB. Contextualising primate origins--an ecomorphological framework. J Anat 2016; 228:608-29. [PMID: 26830706 PMCID: PMC4804135 DOI: 10.1111/joa.12441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 12/15/2022] Open
Abstract
Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins.
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Affiliation(s)
| | - Jeroen B Smaers
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
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