1
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Toussaint EFA, Gauthier J, Bilat J, Gillett CPDT, Gough HM, Lundkvist H, Blanc M, Muñoz-Ramírez CP, Alvarez N. HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution. Genome Biol Evol 2021; 13:6275686. [PMID: 33988685 PMCID: PMC8480185 DOI: 10.1093/gbe/evab112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
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Affiliation(s)
| | | | - Julia Bilat
- Natural History Museum of Geneva, Switzerland
| | - Conrad P D T Gillett
- University of Hawai'i Insect Museum, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Harlan M Gough
- Florida Natural History Museum, University of Florida, Gainesville, Florida, USA
| | | | | | - Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Chile
| | - Nadir Alvarez
- Natural History Museum of Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Switzerland
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2
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Trichas A, Smirli M, Papadopoulou A, Anastasiou I, Keskin B, Poulakakis N. Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Abstract
The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.
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Affiliation(s)
- Apostolos Trichas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Maria Smirli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioannis Anastasiou
- Section of Zoology – Marine Biology, Department of Biology, University of Athens, Panepistimioupoli, GR-157 84 Athens, Greece
| | - Bekir Keskin
- Zoology Department, Section of Biology, Faculty of Science, Ege University, Bornova-Izmir, Turkey
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
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3
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Tao Q, Tamura K, Mello B, Kumar S. Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times. Mol Biol Evol 2020; 37:280-290. [PMID: 31638157 DOI: 10.1093/molbev/msz236] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.
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Affiliation(s)
- Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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4
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Dates and rates in grape's plastomes: evolution in slow motion. Curr Genet 2019; 66:123-140. [PMID: 31201544 DOI: 10.1007/s00294-019-01004-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 01/08/2023]
Abstract
The family Vitaceae includes the domesticated grapevine (Vitis vinifera), one of the most economically important crops in the world. Despite the importance of Vitaceae, there is still considerable controversy surrounding their phylogenetic relationships and evolutionary timescales. Moreover, variation in rates of molecular evolution among Vitaceae remains mostly unexplored. The present research aims to fill these knowledge gaps through the analysis of plastome sequences. Thirteen newly sequenced grape plastomes are presented and their phylogenetic relationships examined. Divergence times and absolute substitution rates are inferred under different molecular clocks by the analysis of 95 non-coding plastid regions and 43 representative accessions of the major lineages of Vitaceae. Furthermore, the phylogenetic informativeness of non-coding plastid regions is investigated. We find strong evidence in favor of the random local clock model and rate heterogeneity within Vitaceae. Substitution rates decelerate in Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, and Vitis, with genus Vitis showing the lowest values up to a minimum of ~ 4.65 × 10-11 s/s/y. We suggest that liana-like species of Vitaceae evolve slower than erect growth habit plants and we invoke the "rate of mitosis hypothesis" to explain the observed pattern of the substitution rates. We identify a reduced set of 20 non-coding regions able to accurately reconstruct the phylogeny of Vitaceae and we provide a detailed description of all 152 non-coding regions identified in the plastomes of subg. Vitis. These polymorphic regions will find their applications in phylogenetics, phylogeography, and population genetics as well in grapes identification through DNA barcoding techniques.
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5
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When did anoles diverge? An analysis of multiple dating strategies. Mol Phylogenet Evol 2018; 127:655-668. [DOI: 10.1016/j.ympev.2018.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/27/2018] [Accepted: 06/06/2018] [Indexed: 11/17/2022]
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6
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Faille A, Casale A, Hernando C, Aït Mouloud S, Ribera I. Tectonic vicariance versus Messinian dispersal in western Mediterranean ground beetles. ZOOL SCR 2018. [DOI: 10.1111/zsc.12301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arnaud Faille
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
- MECADEV-UMR 7179 MNHN/CNRS; Paris France
| | - Achille Casale
- Dipartimento di Scienze della Natura edel Territorio (Zoologia); Sassari. Private; Torino Italy
| | | | | | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
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7
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Toussaint Fls EFA, Gillett CPDT. Rekindling Jeannel’s Gondwanan vision? Phylogenetics and evolution of Carabinae with a focus on Calosoma caterpillar hunter beetles. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Andújar C, Pérez‐González S, Arribas P, Zaballos JP, Vogler AP, Ribera I. Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles. Mol Ecol 2017; 26:6053-6070. [DOI: 10.1111/mec.14358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/23/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Carmelo Andújar
- Department of Life Sciences Natural History Museum London UK
- Department of Life Sciences Imperial College London Ascot UK
- Grupo de Ecología y Evolución en Islas Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain
| | - Sergio Pérez‐González
- Departamento de Zoología y Antropología Física Universidad Complutense de Madrid Madrid Spain
| | - Paula Arribas
- Department of Life Sciences Natural History Museum London UK
- Department of Life Sciences Imperial College London Ascot UK
- Grupo de Ecología y Evolución en Islas Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) San Cristóbal de la Laguna Spain
| | - Juan P. Zaballos
- Departamento de Zoología y Antropología Física Universidad Complutense de Madrid Madrid Spain
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London UK
- Department of Life Sciences Imperial College London Ascot UK
| | - Ignacio Ribera
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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9
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Andújar C, Faille A, Pérez-González S, Zaballos JP, Vogler AP, Ribera I. Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles. Mol Phylogenet Evol 2016; 99:235-246. [DOI: 10.1016/j.ympev.2016.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
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10
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Schenk JJ. Consequences of Secondary Calibrations on Divergence Time Estimates. PLoS One 2016; 11:e0148228. [PMID: 26824760 PMCID: PMC4732660 DOI: 10.1371/journal.pone.0148228] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/14/2016] [Indexed: 11/19/2022] Open
Abstract
Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.
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Affiliation(s)
- John J. Schenk
- Department of Biology, Georgia Southern University, Statesboro, Georgia, United States of America
- * E-mail:
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11
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De Baets K, Dentzien-Dias P, Upeniece I, Verneau O, Donoghue PCJ. Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence. ADVANCES IN PARASITOLOGY 2015; 90:93-135. [PMID: 26597066 DOI: 10.1016/bs.apar.2015.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms.
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Affiliation(s)
- Kenneth De Baets
- Fachgruppe PaläoUmwelt, GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Paula Dentzien-Dias
- Núcleo de Oceanografia Geológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Ieva Upeniece
- Department of Geology, University of Latvia, Riga, Latvia
| | - Olivier Verneau
- Centre de Formation et de Recherche sur les Environnements Méditerranéens, University of Perpignan Via Domitia, Perpignan, France; CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France; Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Science Building, Bristol, UK
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12
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Warnock RCM, Parham JF, Joyce WG, Lyson TR, Donoghue PCJ. Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc Biol Sci 2015; 282:20141013. [PMID: 25429012 PMCID: PMC4262156 DOI: 10.1098/rspb.2014.1013] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.
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Affiliation(s)
- Rachel C M Warnock
- School of Earth Sciences, University of Bristol, Bristol, UK National Evolutionary Synthesis Center, Durham, NC, USA Department of Paleobiology, Smithsonian Institution, Washington DC, USA
| | - James F Parham
- John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg/Freiburg, Switzerland
| | - Tyler R Lyson
- Denver Museum of Nature and Science, Denver, CO, USA
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13
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Montelongo T, Gómez-Zurita J. Multilocus molecular systematics and evolution in time and space ofCalligrapha(Coleoptera: Chrysomelidae, Chrysomelinae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tinguaro Montelongo
- Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
| | - Jesús Gómez-Zurita
- Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
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14
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Andújar C, Arribas P, Ruiz C, Serrano J, Gómez-Zurita J. Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation ofMesocarabus(Coleoptera: Carabidae). Mol Ecol 2014; 23:4344-61. [DOI: 10.1111/mec.12793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. Andújar
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - P. Arribas
- Departamento de Ecología e Hidrología; Facultad de Biología; Universidad de Murcia; Murcia 30100 Spain
| | - C. Ruiz
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
- Departamento de Ciencias Naturales; Universidad Técnica Particular de Loja; San Cayetano Alto s/n C.P. 11 01 608 Loja Ecuador
| | - J. Serrano
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - J. Gómez-Zurita
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 Barcelona 08003 Spain
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15
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Duchêne S, Lanfear R, Ho SYW. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol Phylogenet Evol 2014; 78:277-89. [PMID: 24910154 DOI: 10.1016/j.ympev.2014.05.032] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/16/2014] [Accepted: 05/28/2014] [Indexed: 11/26/2022]
Abstract
Phylogenetic estimates of evolutionary timescales can be obtained from nucleotide sequence data using the molecular clock. These estimates are important for our understanding of evolutionary processes across all taxonomic levels. The molecular clock needs to be calibrated with an independent source of information, such as fossil evidence, to allow absolute ages to be inferred. Calibration typically involves fixing or constraining the age of at least one node in the phylogeny, enabling the ages of the remaining nodes to be estimated. We conducted an extensive simulation study to investigate the effects of the position and number of calibrations on the resulting estimate of the timescale. Our analyses focused on Bayesian estimates obtained using relaxed molecular clocks. Our findings suggest that an effective strategy is to include multiple calibrations and to prefer those that are close to the root of the phylogeny. Under these conditions, we found that evolutionary timescales could be estimated accurately even when the relaxed-clock model was misspecified and when the sequence data were relatively uninformative. We tested these findings in a case study of simian foamy virus, where we found that shallow calibrations caused the overall timescale to be underestimated by up to three orders of magnitude. Finally, we provide some recommendations for improving the practice of molecular-clock calibration.
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Affiliation(s)
- Sebastián Duchêne
- School of Biological Sciences, University of Sydney, NSW 2006, Australia.
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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