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Mereu P, Pirastru M, Morell Miranda P, Atağ G, Başak Vural K, Wilkens B, Rodrigues Soares AE, Kaptan D, Zedda M, Columbano N, Barbato M, Naitana S, Hadjisterkotis E, Somel M, Özer F, Günther T, Leoni GG. Revised phylogeny of mouflon based on expanded sampling of mitogenomes. PLoS One 2025; 20:e0323354. [PMID: 40367058 PMCID: PMC12077669 DOI: 10.1371/journal.pone.0323354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 04/07/2025] [Indexed: 05/16/2025] Open
Abstract
Mouflons are flagship species of the Mediterranean islands where they persist. Once thought to be the remnants of a European wild sheep population, archaeology suggests they were introduced by humans to the islands of Cyprus in the Early Neolithic (~10,000 years ago) and later to Corsica and Sardinia. Their status as truly wild animals remains a subject of debate. To investigate the phylogenetic relationship between these island populations and other domestic and wild sheep from the Mediterranean region, we sequenced 50 mitogenomes of mouflons from Sardinia and Corsica, and modern and ancient Sardinian domestic sheep. A total of 68 additional publicly available mitogenomes were included in the comparative analysis and used to reconstruct the phylogeny of sheep and its closest wild relative, the mouflon (Ovis gmelini). Our study analyzed the evolutionary relationships within the C-E-X and haplogroup B clusters, showing that: a) Cyprus mouflons are more related to Anatolian and Iranian mouflons belonging to the wild haplogroup X, which seems to be basal to the domestic C and E haplogroups; b) Corsican and Sardinian mouflon arise from basal lineages associated with the early European expansion of domestic sheep. These results highlight the phylogenetic distinctiveness of the mouflon populations from the Mediterranean islands, suggesting a revision of their systematic classification and an update of the nomenclature for Sardinian and Corsican mouflons from the current status of subspecies of domestic sheep (Ovis aries musimon) to subspecies of their wild relatives (Ovis gmelini musimon) which would facilitate conservation efforts.
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Affiliation(s)
- Paolo Mereu
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Monica Pirastru
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Pedro Morell Miranda
- Human Evolution Program, Institute for Organismal Biology, Uppsala University, Uppsala, Sweden
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Gözde Atağ
- Department of Biological Sciences, Biology/Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Biology/Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | | | | | - Damla Kaptan
- Department of Biological Sciences, Biology/Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Marco Zedda
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicolò Columbano
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Mario Barbato
- Department of Veterinary Sciences, Università degli Studi di Messina, Messina, Italy
| | - Salvatore Naitana
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Eleftherios Hadjisterkotis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Mehmet Somel
- Department of Biological Sciences, Biology/Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Faculty of Letters, Hacettepe University, Ankara, Turkey
- Department of Social Anthropology, Hacettepe University, Ankara, Turkey
| | - Torsten Günther
- Human Evolution Program, Institute for Organismal Biology, Uppsala University, Uppsala, Sweden
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Rodrigues-Oliveira IH, Batista da Silva I, Rocha RR, Soares RAS, Menegidio FB, Garcia C, Pasa R, Kavalco KF. When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats' species (Felidae: Machairodontinae). Mitochondrial DNA A DNA Mapp Seq Anal 2025; 35:102-110. [PMID: 39644159 DOI: 10.1080/24701394.2024.2439433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 12/02/2024] [Indexed: 12/09/2024]
Abstract
Within the Machairodontinae subfamily, commonly referred to as saber-toothed cats, it is worth noting that only two species, namely Homotherium latidens, recognized as the scimitar-toothed cat, and Smilodon populator, renowned as the saber-toothed tiger, possess partial mitochondrial genomes accessible in the NCBI database. These sequences, however, do not include the mitogenome control region (mtDNA control region) and have several gaps in their genes, including protein-coding genes (PCGs) that are widely used in phylogenetic analysis. In this study, we aimed to obtain a complete assembly of the mitogenomes of these two species from next-generation sequencing data available at NCBI's SRA. The de novo assemblies showed complete mitogenomes with 17,323bp (H. latidens) and 16,769 bp (S. populator), both with 13 PCGs, 22tRNAs, two rRNAs and the mtDNA control region, with all genes following the standard order and position of most vertebrate mitogenomes. Despite being generally very similar to previous studies, our phylogeny and molecular dating reveals an earliest divergence between North American and North Sea H. latidens specimens which may be related to an Early Pleistocene migration across Beringia.
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Affiliation(s)
- Igor Henrique Rodrigues-Oliveira
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
| | - Iuri Batista da Silva
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
| | - Renan Rodrigues Rocha
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Technological Research Center, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil
| | - Rafael Augusto Silva Soares
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
| | | | - Caroline Garcia
- Laboratory of Cytogenetics, University of the State of Bahia Campus Jequié, Jequié, Bahia, Brazil
| | - Rubens Pasa
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, Minas Gerais, Brazil
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3
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Brevet M, Lartillot N. Reconstructing the History of Variation in Effective Population Size along Phylogenies. Genome Biol Evol 2021; 13:6311658. [PMID: 34190972 PMCID: PMC8358220 DOI: 10.1093/gbe/evab150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
The nearly neutral theory predicts specific relations between effective population size (Ne) and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward, owing to the difficulty in estimating Ne. Here, we introduce an integrative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly neutral theory and an estimation of the allometric scaling of the ratios of nonsynonymous over synonymous polymorphism (πN/πS) and divergence (dN/dS) with respect to Ne. As an illustration, we applied our method to primates, for which the nearly neutral predictions were mostly verified. Under a purely nearly neutral model with a constant DFE across species, we find that the variation in πN/πS and dN/dS as a function of Ne is too large to be compatible with current estimates of the DFE based on site frequency spectra. The reconstructed history of Ne shows a 10-fold variation across primates. The mutation rate per generation u, also reconstructed over the tree by the method, varies over a 3-fold range and is negatively correlated with Ne. As a result of these opposing trends for Ne and u, variation in πS is intermediate, primarily driven by Ne but substantially influenced by u. Altogether, our integrative framework provides a quantitative assessment of the role of Ne and u in modulating patterns of genetic variation, while giving a synthetic picture of their history over the clade.
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Affiliation(s)
- Mathieu Brevet
- Station d'Écologie Théorique et Expérimentale, UPR 2001, Moulis, France
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France
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Mortz M, Levivier A, Lartillot N, Dufresne F, Blier PU. Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates. Front Mol Biosci 2021; 8:626042. [PMID: 33791336 PMCID: PMC8005583 DOI: 10.3389/fmolb.2021.626042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023] Open
Abstract
Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.
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Affiliation(s)
- Mathieu Mortz
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Aurore Levivier
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Nicolas Lartillot
- Laboratoire De Biométrie et Biologie Evolutive, UMR CNRS, Université Lyon 1, Villeurbanne, France
| | - France Dufresne
- Laboratoire D'écologie Moléculaire, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada.,Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Pierre U Blier
- Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
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5
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Gong M, Shafer ABA, Hu X, Huang Y, Zhang L, Li H, Wu Y, Wen W, Liu G. Population demographic history and adaptability of the vulnerable Lolokou Sucker Frog. Genetica 2020; 148:207-213. [PMID: 33052504 DOI: 10.1007/s10709-020-00105-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 09/26/2020] [Indexed: 11/30/2022]
Abstract
Amphibians are experiencing worldwide declines due to increasing anthropogenetic disturbances. However, the genetic variability and hence adaptability are still unknown for most frogs. We integrated the mitochondrial (ND2 gene), nuclear (TYR gene) and major histocompatibility complex (MHC) loci, to clarify the demographic patterns and immune-gene diversity of the Lolokou Sucker Frog (Amolops loloensis). Demographic analysis of the ND2 and TYR genes suggested that the Lolokou Sucker Frog experienced a population expansion within the last 10,000 years. High MHC diversity was detected, which has likely resulted from positive selection, indicating the current diversity bodes well for the species' adaptive potential to pathogenic challenges. These findings broaden our knowledge on the population history and evolution adaptation of the reclusive torrent frog, and conservation implications are provided.
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Affiliation(s)
- Minghao Gong
- Institute of Wetland Research, Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, 100091, China
| | - Aaron B A Shafer
- Forensics & Environmental and Life Sciences, Trent University, Peterborough, 7K9J 7B8, Canada
| | - Xiaolong Hu
- College of Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yaohua Huang
- Mabian Dafengding National Nature Reserve, Sichuan, 614600, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Huixin Li
- Institute of Wetland Research, Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ye Wu
- Mabian Dafengding National Nature Reserve, Sichuan, 614600, China
| | - Wanyu Wen
- Institute of Wetland Research, Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, 100091, China
| | - Gang Liu
- Institute of Wetland Research, Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, 100091, China.
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Ben Chehida Y, Thumloup J, Schumacher C, Harkins T, Aguilar A, Borrell A, Ferreira M, Rojas-Bracho L, Robertson KM, Taylor BL, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Sci Rep 2020; 10:15190. [PMID: 32938978 PMCID: PMC7494866 DOI: 10.1038/s41598-020-71603-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Cassie Schumacher
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Timothy Harkins
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Alex Aguilar
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Asunción Borrell
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Marisa Ferreira
- MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080-530, Figueira da Foz, Portugal.,CPRAM-Ecomare, Estrada Do Porto de Pesca Costeira, 3830-565, Gafanha da Nazaré, Portugal
| | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas (CONANP), C/o Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, BC, Mexico
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Gísli A Víkingsson
- Marine and Freshwater Research Institute, Fornubúðum 5, 220, Hafnarfjörður, Iceland
| | - Arthur Weyna
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Jonathan Romiguier
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands. .,Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche Pour Le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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7
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Lartillot N, Phillips MJ, Ronquist F. A mixed relaxed clock model. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0132. [PMID: 27325829 PMCID: PMC4920333 DOI: 10.1098/rstb.2015.0132] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/13/2022] Open
Abstract
Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, F-69622 Villeurbanne Cedex, France
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 104 05 Stockholm, Sweden
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Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds. Mol Biol Evol 2017; 34:3123-3131. [DOI: 10.1093/molbev/msx236] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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9
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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10
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Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Mol Biol Evol 2016; 33:1517-27. [DOI: 10.1093/molbev/msw033] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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11
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Tidière M, Gaillard JM, Müller DWH, Lackey LB, Gimenez O, Clauss M, Lemaître JF. Does sexual selection shape sex differences in longevity and senescence patterns across vertebrates? A review and new insights from captive ruminants. Evolution 2015; 69:3123-40. [DOI: 10.1111/evo.12801] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 09/11/2015] [Accepted: 10/11/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Morgane Tidière
- CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622, Université Lyon 1 Villeurbanne France
| | - Jean-Michel Gaillard
- CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622, Université Lyon 1 Villeurbanne France
| | - Dennis W. H. Müller
- Zoological Garden Halle (Saale); Fasanenstr. 5a; 06114 Halle (Saale) Germany
| | | | - Olivier Gimenez
- UMR 5175, Modelling and Conservation, Centre d'Ecologie Fonctionnelle et Evolutive; Campus CNRS; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Marcus Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty; University of Zurich; Winterthurerstr. 260 8057 Zurich Switzerland
| | - Jean-François Lemaître
- CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622, Université Lyon 1 Villeurbanne France
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Abstract
MOTIVATION Brownian models have been introduced in phylogenetics for describing variation in substitution rates through time, with applications to molecular dating or to the comparative analysis of variation in substitution patterns among lineages. Thus far, however, the Monte Carlo implementations of these models have relied on crude approximations, in which the Brownian process is sampled only at the internal nodes of the phylogeny or at the midpoints along each branch, and the unknown trajectory between these sampled points is summarized by simple branchwise average substitution rates. RESULTS A more accurate Monte Carlo approach is introduced, explicitly sampling a fine-grained discretization of the trajectory of the (potentially multivariate) Brownian process along the phylogeny. Generic Monte Carlo resampling algorithms are proposed for updating the Brownian paths along and across branches. Specific computational strategies are developed for efficient integration of the finite-time substitution probabilities across branches induced by the Brownian trajectory. The mixing properties and the computational complexity of the resulting Markov chain Monte Carlo sampler scale reasonably with the discretization level, allowing practical applications with up to a few hundred discretization points along the entire depth of the tree. The method can be generalized to other Markovian stochastic processes, making it possible to implement a wide range of time-dependent substitution models with well-controlled computational precision. AVAILABILITY The program is freely available at www.phylobayes.org.
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Affiliation(s)
- Benjamin Horvilleur
- Université de Lyon, Université Lyon 1, CNRS; UMR 5558, Laboratoire de Biométrie, Biologie Évolutive, F-69622 Villeurbanne, France
| | - Nicolas Lartillot
- Université de Lyon, Université Lyon 1, CNRS; UMR 5558, Laboratoire de Biométrie, Biologie Évolutive, F-69622 Villeurbanne, France
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