1
|
Liu GM, Pan Q, Du J, Zhu PF, Liu WQ, Li ZH, Wang L, Hu CY, Dai YC, Zhang XX, Zhang Z, Yu Y, Li M, Wang PC, Wang X, Li M, Zhou XM. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zool Res 2023; 44:1064-1079. [PMID: 37914522 PMCID: PMC10802097 DOI: 10.24272/j.issn.2095-8137.2023.189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023] Open
Abstract
The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.
Collapse
Affiliation(s)
- Gao-Ming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping-Fen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Qiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Hao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Yan Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Chen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Xiao Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng-Cheng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu-Ming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
| |
Collapse
|
2
|
Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
Collapse
Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| |
Collapse
|
3
|
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
| |
Collapse
|
4
|
Plattner H. Ciliate Research. From Myth to Trendsetting Science. J Eukaryot Microbiol 2022; 69:e12926. [PMID: 35608570 DOI: 10.1111/jeu.12926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
This special issue of the Journal of Eukaryotic Microbiology (JEM) summarizes achievements obtained by generations of researchers with ciliates in widely different disciplines. In fact, ciliates range among the first cells seen under the microscope centuries ago. Their beauty made them an object of scientia amabilis and their manifold reactions made them attractive for college experiments and finally challenged causal analyses at the cellular level. Some of this work was honored by a Nobel Prize. Some observations yielded a baseline for additional novel discoveries, occasionally facilitated by specific properties of some ciliates. This also offers some advantage in the exploration of closely related parasites (malaria). Articles contributed here by colleagues from all over the world encompass a broad spectrum of ciliate life, from genetics to evolution, from molecular cell biology to ecology, from intercellular signaling to epigenetics etc. This introductory chapter, largely based on my personal perception, aims at integrating work presented in this special issue of JEM into a broader historical context up to current research.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Baleka S, Varela L, Tambusso PS, Paijmans JL, Mothé D, Stafford TW, Fariña RA, Hofreiter M. Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA. iScience 2022; 25:103559. [PMID: 34988402 PMCID: PMC8693454 DOI: 10.1016/j.isci.2021.103559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 01/13/2023] Open
Abstract
The extinct Gomphotheriidae is the only proboscidean family that colonized South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, ancient DNA (aDNA) preservation decreases in warmer regions. Despite the poor preservation conditions for aDNA in humid, sub-tropical climates, we recovered ∼3,000 bp of mtDNA of Notiomastodon platensis from the Arroyo del Vizcaíno site, Uruguay. Our calibrated phylogeny places Notiomastodon as a sister taxon to Elephantidae, with a divergence time of ∼13.5 Ma. Additionally, a total evidence analysis combining morphological and paleogenetic data shows that the three most diverse clades within Proboscidea diverged during the early Miocene, coinciding with the formation of a land passage between Africa and Eurasia. Our results are a further step toward aDNA analyses on Pleistocene samples from subtropical regions and provide a framework for proboscidean evolution.
Collapse
Affiliation(s)
- Sina Baleka
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargata 2, 102 Reykjavik, Iceland
| | - Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - P. Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - Johanna L.A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Dimila Mothé
- Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro, Av. Pasteur, 458/501, 22290-240 Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biodiversidade e Biologia Evolutiva, Centro de Ciências da Saúde, Instituto de Biologia, Campus Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Richard A. Fariña
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| |
Collapse
|
7
|
Barba-Montoya J, Tao Q, Kumar S. Molecular and morphological clocks for estimating evolutionary divergence times. BMC Ecol Evol 2021; 21:83. [PMID: 33980146 PMCID: PMC8117668 DOI: 10.1186/s12862-021-01798-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. RESULTS We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data. CONCLUSIONS Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.
Collapse
Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
8
|
Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 2019; 17:e3000494. [PMID: 31800571 PMCID: PMC6892540 DOI: 10.1371/journal.pbio.3000494] [Citation(s) in RCA: 493] [Impact Index Per Article: 98.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
Collapse
Affiliation(s)
- Nathan S. Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Jacob A. Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Caldas IV, Schrago CG. Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock. Ecol Evol 2019; 9:2255-2262. [PMID: 30847109 PMCID: PMC6392387 DOI: 10.1002/ece3.4921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 01/17/2023] Open
Abstract
Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K-Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short-fuse hypothesis.
Collapse
Affiliation(s)
- Ian V. Caldas
- Department of GeneticsFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Carlos G. Schrago
- Department of GeneticsFederal University of Rio de JaneiroRio de JaneiroBrazil
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS, Université de Montpellier, Montpellier, France
| |
Collapse
|
12
|
Varela L, Tambusso PS, McDonald HG, Fariña RA. Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis. Syst Biol 2018; 68:204-218. [DOI: 10.1093/sysbio/syy058] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 09/10/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - P Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - H Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South, Salt Lake City, UT 84101 USA
| | - Richard A Fariña
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| |
Collapse
|
13
|
Kurabi A, Schaerer D, Noack V, Bernhardt M, Pak K, Alexander T, Husseman J, Nguyen Q, Harris JP, Ryan AF. Active Transport of Peptides Across the Intact Human Tympanic Membrane. Sci Rep 2018; 8:11815. [PMID: 30087425 PMCID: PMC6081404 DOI: 10.1038/s41598-018-30031-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022] Open
Abstract
We previously identified peptides that are actively transported across the intact tympanic membrane (TM) of rats with infected middle ears. To assess the possibility that this transport would also occur across the human TM, we first developed and validated an assay to evaluate transport in vitro using fragments of the TM. Using this assay, we demonstrated the ability of phage bearing a TM-transiting peptide to cross freshly dissected TM fragments from infected rats or from uninfected rats, guinea pigs and rabbits. We then evaluated transport across fragments of the human TM that were discarded during otologic surgery. Human trans-TM transport was similar to that seen in the animal species. Finally, we found that free peptide, unconnected to phage, was transported across the TM at a rate comparable to that seen for peptide-bearing phage. These studies provide evidence supporting the concept of peptide-mediated drug delivery across the intact TM and into the middle ears of patients.
Collapse
Affiliation(s)
- Arwa Kurabi
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA.
- San Diego Veterans Affairs Healthcare System, Research Department, San Diego, CA, 92130, USA.
| | - Daniel Schaerer
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
| | - Volker Noack
- Ruhr-Universitat Bochum, Department of ENT, Bochum, NRW, Germany
| | - Marlen Bernhardt
- Universitätsklinik Würzburg, Department of ENT, Würzburg, 97070, Germany
| | - Kwang Pak
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
- San Diego Veterans Affairs Healthcare System, Research Department, San Diego, CA, 92130, USA
| | - Thomas Alexander
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
| | - Jacob Husseman
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
| | - Quyen Nguyen
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
| | - Jeffrey P Harris
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
| | - Allen F Ryan
- University of California, San Diego, Division of Otolaryngology, Department of Surgery, La Jolla, CA, 92093, USA
- San Diego Veterans Affairs Healthcare System, Research Department, San Diego, CA, 92130, USA
| |
Collapse
|
14
|
Schrago CG, Aguiar BO, Mello B. Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data. J Evol Biol 2018; 31:1477-1484. [DOI: 10.1111/jeb.13344] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Carlos G. Schrago
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Barbara O. Aguiar
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Beatriz Mello
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| |
Collapse
|
15
|
Motani R, Jiang DY, Tintori A, Ji C, Huang JD. Pre- versus post-mass extinction divergence of Mesozoic marine reptiles dictated by time-scale dependence of evolutionary rates. Proc Biol Sci 2018; 284:rspb.2017.0241. [PMID: 28515201 DOI: 10.1098/rspb.2017.0241] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
The fossil record of a major clade often starts after a mass extinction even though evolutionary rates, molecular or morphological, suggest its pre-extinction emergence (e.g. squamates, placentals and teleosts). The discrepancy is larger for older clades, and the presence of a time-scale-dependent methodological bias has been suggested, yet it has been difficult to avoid the bias using Bayesian phylogenetic methods. This paradox raises the question of whether ecological vacancies, such as those after mass extinctions, prompt the radiations. We addressed this problem by using a unique temporal characteristic of the morphological data and a high-resolution stratigraphic record, for the oldest clade of Mesozoic marine reptiles, Ichthyosauromorpha. The evolutionary rate was fastest during the first few million years of ichthyosauromorph evolution and became progressively slower over time, eventually becoming six times slower. Using the later slower rates, estimates of divergence time become excessively older. The fast, initial rate suggests the emergence of ichthyosauromorphs after the end-Permian mass extinction, matching an independent result from high-resolution stratigraphic confidence intervals. These reptiles probably invaded the sea as a new ecosystem was formed after the end-Permian mass extinction. Lack of information on early evolution biased Bayesian clock rates.
Collapse
Affiliation(s)
- Ryosuke Motani
- Department of Earth and Planetary Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Da-Yong Jiang
- Department of Geology and Geological Museum, Peking University, Yiheyuan Street 5, Beijing 100871, People's Republic of China.,State Key Laboratory of Palaeobiology and Stratigraphy (Nanjing Institute of Geology and Palaeontology), 39 East Beijing Road, Nanjing 210008, People's Republic of China
| | - Andrea Tintori
- Dipartimento di Scienze della Terra, Università degli Studi di Milano, Via Mangiagalli 34-20133 Milano, Italy
| | - Cheng Ji
- Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing 210008, People's Republic of China
| | - Jian-Dong Huang
- Department of Research, Anhui Geological Museum, Jiahe Road 999, Hefei, Anhui 230031, People's Republic of China
| |
Collapse
|
16
|
Goloboff PA, Torres A, Arias JS. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 2017; 34:407-437. [DOI: 10.1111/cla.12205] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2017] [Indexed: 11/28/2022] Open
Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
| | - Ambrosio Torres
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
| | - J. Salvador Arias
- Unidad Ejecutora Lillo; Fundación Miguel Lillo; CONICET; Miguel Lillo 251 4000 San Miguel de Tucumán Argentina
| |
Collapse
|
17
|
Harrington SM, Reeder TW. Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw039] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
18
|
Turner AH, Pritchard AC, Matzke NJ. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades. PLoS One 2017; 12:e0169885. [PMID: 28187191 PMCID: PMC5302793 DOI: 10.1371/journal.pone.0169885] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
Collapse
Affiliation(s)
- Alan H. Turner
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Adam C. Pritchard
- Department of Geology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| |
Collapse
|