1
|
Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
Collapse
Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| |
Collapse
|
2
|
Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024; 39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [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: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.
Collapse
Affiliation(s)
- Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
| |
Collapse
|
3
|
Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
Collapse
Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| |
Collapse
|
4
|
Trevine VC, Grazziotin FG, Giraudo A, Sallesbery‐Pinchera N, Vianna JA, Zaher H. The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence. ZOOL SCR 2022. [DOI: 10.1111/zsc.12565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Vivian C. Trevine
- Laboratório de Coleções Zoológicas Instituto Butantan São Paulo Brazil
- Programa de Pós‐Graduação de Zoologia, Insituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Alejandro Giraudo
- Instituto Nacional de Limnología (CONICET – UNL) Ciudad Universitaria Santa Fe Argentina
- Facultad de Humanidades y Ciencias (FHUC – UNL) Ciudad Universitaria Santa Fe Argentina
| | - Nicole Sallesbery‐Pinchera
- Escuela Medicina Veterinaria, Facultad Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Juliana A. Vianna
- Millennium Institute Center for Genome Regulation (CRG), Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Hussam Zaher
- Laboratório de Herpetologia, Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
| |
Collapse
|
5
|
Molecular phylogenies map to biogeography better than morphological ones. Commun Biol 2022; 5:521. [PMID: 35641555 PMCID: PMC9156683 DOI: 10.1038/s42003-022-03482-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable. Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.
Collapse
|
6
|
Orr RJS, Di Martino E, Ramsfjell MH, Gordon DP, Berning B, Chowdhury I, Craig S, Cumming RL, Figuerola B, Florence W, Harmelin JG, Hirose M, Huang D, Jain SS, Jenkins HL, Kotenko ON, Kuklinski P, Lee HE, Madurell T, McCann L, Mello HL, Obst M, Ostrovsky AN, Paulay G, Porter JS, Shunatova NN, Smith AM, Souto-Derungs J, Vieira LM, Voje KL, Waeschenbach A, Zágoršek K, Warnock RCM, Liow LH. Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny. SCIENCE ADVANCES 2022; 8:eabm7452. [PMID: 35353568 PMCID: PMC8967238 DOI: 10.1126/sciadv.abm7452] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.
Collapse
Affiliation(s)
| | | | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Björn Berning
- Geoscience Collections, Oberösterreichische Landes-Kultur GmbH, Linz, Austria
| | - Ismael Chowdhury
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Sean Craig
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | | | - Wayne Florence
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa
| | - Jean-Georges Harmelin
- Station marine d’Endoume, OSU Pytheas, MIO, GIS Posidonie, Université Aix-Marseille, Marseille, France
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sudhanshi S. Jain
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Helen L. Jenkins
- Marine Biological Association of the UK, Plymouth, UK
- Natural History Museum, London, UK
| | - Olga N. Kotenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Piotr Kuklinski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Hannah E. Lee
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | - Linda McCann
- Smithsonian Environmental Research Center, TIburon, CA, USA
| | | | - Matthias Obst
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew N. Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Gustav Paulay
- Florida Museum of Natural History, Gainesville, FL, USA
| | - Joanne S. Porter
- International Centre for Island Technology, Heriot-Watt University, Stromness, UK
| | - Natalia N. Shunatova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Javier Souto-Derungs
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Leandro M. Vieira
- Natural History Museum, London, UK
- Department of Zoology, Universidade Federal de Pernambuco, Recife, Brazil
| | - Kjetil L. Voje
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Liberec, Czech Republic
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
7
|
Asher RJ, Smith MR. Phylogenetic Signal and Bias in Paleontology. Syst Biol 2021; 71:986-1008. [PMID: 34469583 PMCID: PMC9248965 DOI: 10.1093/sysbio/syab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.
Collapse
Affiliation(s)
- Robert J Asher
- Department of Zoology, Downing St., University of Cambridge CB2 3EJ, UK
| | - Martin R Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
| |
Collapse
|
8
|
Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
| | | |
Collapse
|
9
|
Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
Collapse
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| |
Collapse
|
10
|
Orr RJS, Di Martino E, Gordon DP, Ramsfjell MH, Mello HL, Smith AM, Liow LH. A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution. Mol Phylogenet Evol 2021; 161:107172. [PMID: 33813020 DOI: 10.1016/j.ympev.2021.107172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, and 17 genes (2 nuclear and 15 mitochondrial) we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified body-wall layer in ascus-bearing cheilostomes) and ask if its presence has any bearing on the diversification rates of cheilostomes.
Collapse
Affiliation(s)
- R J S Orr
- Natural History Museum, University of Oslo, Oslo, Norway.
| | - E Di Martino
- Natural History Museum, University of Oslo, Oslo, Norway
| | - D P Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - M H Ramsfjell
- Natural History Museum, University of Oslo, Oslo, Norway
| | - H L Mello
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - A M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - L H Liow
- Natural History Museum, University of Oslo, Oslo, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
11
|
Maruyama SR, Rogerio LA, Freitas PD, Teixeira MMG, Ribeiro JMC. Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes. Sci Rep 2021; 11:3791. [PMID: 33589693 PMCID: PMC7884790 DOI: 10.1038/s41598-021-81926-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.
Collapse
Affiliation(s)
- Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil.
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Patricia Domingues Freitas
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | | | - José Marcos Chaves Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway rm 2E32, Rockville, MD, 20852, USA.
| |
Collapse
|
12
|
Neumann JS, Desalle R, Narechania A, Schierwater B, Tessler M. Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets. Syst Biol 2021; 70:360-375. [PMID: 32462193 PMCID: PMC7875439 DOI: 10.1093/sysbio/syaa038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].
Collapse
Affiliation(s)
- Johannes S Neumann
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Rob Desalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Bernd Schierwater
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- ITZ, Division of Ecology and Evolution, Tierärztliche Hochschule Hannover, Bünteweg 9, 30559 Hannover, Germany
| | - Michael Tessler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| |
Collapse
|
13
|
Mongiardino Koch N, Thompson JR. A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data. Syst Biol 2020; 70:421-439. [PMID: 32882040 DOI: 10.1093/sysbio/syaa069] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].
Collapse
Affiliation(s)
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
14
|
Crouch NMA, Mason-Gamer R. Mass estimation of extinct taxa and phylogenetic hypotheses both influence analyses of character evolution in a large clade of birds (Telluraves). Proc Biol Sci 2019; 286:20191745. [PMID: 31847761 DOI: 10.1098/rspb.2019.1745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Incorporating extinct taxa in phylogenetic comparative methods is rapidly becoming invaluable in studies of character evolution. An increasing number of studies have evaluated the effects of extinct taxa, and different numbers of extinct taxa, on model selection and parameter estimation. Body mass is a well-studied phenotype, but individual mass estimates may vary dramatically depending on the particular measurement used. Here, we perform an analysis of body mass evolution in a large clade of principally arboreal birds, incorporating 76 extinct species. We evaluate how different methods for estimating body mass of extinct taxa, and different phylogenetic hypotheses, affect our understanding of the rate and pattern of body mass evolution. Our results show that model selection can vary dramatically depending on the phenotypic and phylogenetic hypothesis used in the reconstruction. Even small changes in phenotype estimates can lead to different model selection and, as a result, affect the inferred evolutionary history. The best-fit models support an increase in the rate of evolution following the K-Pg boundary, with variation accumulating linearly through the Cenozoic. These results provide additional insight into the application of comparative models of evolution, as well as the evolutionary history of one of the most spectacular vertebrate radiations.
Collapse
Affiliation(s)
- Nicholas M A Crouch
- Department of Geological Sciences, University of Texas at Austin, Austin, TX 78756, USA
| | - Roberta Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
15
|
Wilcox JJS, Boissinot S, Idaghdour Y. Falcon genomics in the context of conservation, speciation, and human culture. Ecol Evol 2019; 9:14523-14537. [PMID: 31938538 PMCID: PMC6953694 DOI: 10.1002/ece3.5864] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/11/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Here, we review the diversity, evolutionary history, and genomics of falcons in the context of their conservation and interactions with humans, and provide a perspective on how new genomic approaches may be applied to expand our knowledge of these topics. For millennia, humans and falcons (genus Falco) have developed unique relationships through falconry, religious rituals, conservation efforts, and human lifestyle transitions. From an evolutionary perspective, falcons remain an enigma. Having experienced several recent radiations, they have reached an unparalleled and almost global distribution, with an intrageneric species richness that is roughly an order of magnitude higher than typical within their family (Falconidae) and across other birds (Phylum: Aves). This diversity has evolved in the context of unusual genomic architecture that includes unique chromosomal rearrangements, relatively low chromosome counts, extremely low microdeletion rates, and high levels of nuclear mitochondrial DNA segments (NUMTs). These genomic peculiarities combine with high levels of ecological and organismal diversity and a legacy of human interactions to make falcons obvious candidates for evolutionary studies, providing unique research opportunities in common topics, including chromosomal evolution, the mechanics of speciation, local adaptation, domestication, and urban adaptation.
Collapse
Affiliation(s)
- Justin J. S. Wilcox
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Stéphane Boissinot
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
- Program in BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Youssef Idaghdour
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
- Program in BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| |
Collapse
|
16
|
Cabra-García J, Hormiga G. Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.
Collapse
Affiliation(s)
- Jimmy Cabra-García
- Departamento de Biología, Universidad del Valle, Cali, AA, Colombia
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo Hormiga
- The George Washington University, Department of Biological Sciences, Washington, DC, USA
| |
Collapse
|
17
|
Jana A, Karanth P. Multilocus nuclear markers provide new insights into the origin and evolution of the blackbuck (Antilope cervicapra, Bovidae). Mol Phylogenet Evol 2019; 139:106560. [DOI: 10.1016/j.ympev.2019.106560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 02/02/2023]
|
18
|
Pie MR, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE. Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest. Mol Phylogenet Evol 2019; 141:106627. [PMID: 31539606 DOI: 10.1016/j.ympev.2019.106627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/17/2019] [Accepted: 09/17/2019] [Indexed: 10/26/2022]
Abstract
The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.
Collapse
Affiliation(s)
- Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil.
| | - Marcos R Bornschein
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Instituto de Biociências, Universidade Estadual Paulista, Praça Infante Dom Henrique s/no, Parque Bitaru, CEP 11330-900 São Vicente, São Paulo, Brazil
| | - Luiz F Ribeiro
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Escola de Ciências da Vida, Pontifícia Universidade Católica do Paraná, CEP 80215-901 Curitiba, Paraná, Brazil
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
| |
Collapse
|
19
|
Sookias RB. Exploring the effects of character construction and choice, outgroups and analytical method on phylogenetic inference from discrete characters in extant crocodilians. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Phylogenies for fossil taxa must be inferred from morphology, but accuracy of inference is questionable. Here, morphological characters for extant crocodilians are investigated to assess how to improve inference accuracy. The homoplasy of characters is assessed against a DNA-based phylogenetic tree. Cranial characters are significantly less homoplastic, but this result is perhaps confounded by research effort. Meristic characters are significantly more homoplastic and should be used with caution. Characters were reassessed first hand and documented. Those characters passing tests of robust construction are significantly less homoplastic. Suggestions are made for means to improve coding of discrete characters. Phylogenies inferred using only robust characters and a reassessed matrix, including corrected scorings, were not overall closer to the DNA tree, but did often place the gharial (Gavialis) in a position agreeing with or closer to it. The effects of the choice of analytical method were modest, but Bayesian analysis of the reassessed matrix placed Gavialis and Mecistops (slender-snouted crocodile) in DNA-concordant positions. Use of extant rather than extinct outgroups, even with the original matrix, placed Gavialis in a more DNA-concordant position, as did factoring out 3D skull shape. The morphological case for placement of Gavialis outside other extant crocodilians is arguably overstated, with many characters linked to skull shape.
Collapse
Affiliation(s)
- Roland B Sookias
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße, Berlin, Germany
| |
Collapse
|
20
|
Hołyńska M, Wyngaard GA. Towards a phylogeny of
Cyclops
(Copepoda): (in)congruences among morphology, molecules and zoogeography. ZOOL SCR 2019. [DOI: 10.1111/zsc.12342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Hołyńska
- Museum and Institute of Zoology Polish Academy of Sciences Warszawa Poland
| | - Grace A. Wyngaard
- Department of Biology James Madison University Harrisonburg Virginia
| |
Collapse
|
21
|
Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
Collapse
Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| |
Collapse
|
22
|
Troudet J, Vignes-Lebbe R, Grandcolas P, Legendre F. The Increasing Disconnection of Primary Biodiversity Data from Specimens: How Does It Happen and How to Handle It? Syst Biol 2018; 67:1110-1119. [PMID: 29893962 DOI: 10.1093/sysbio/syy044] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/02/2018] [Indexed: 02/04/2023] Open
Abstract
Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based (OB) occurrences is overthrowing the collection of specimen-based (SB) occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e., SB occurrences) fell from 68% to 18%; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it. Specifically, we emphasize why SB occurrences must be gathered, as a warrant to allow both repeating evolutionary studies and conducting rich and diverse investigations. When impossible to secure, voucher specimens must be replaced with OB occurrences combined with ancillary data (e.g., pictures, recordings, samples, DNA sequences). Ancillary data are instrumental for the usefulness of biodiversity occurrences and we show that, despite improving technologies to collate them, they remain rarely shared. The consequences of such a change are not yet clear but we advocate collecting material evidence or ancillary data to ensure that primary biodiversity data collected lately do not partly become obsolete when doubtful.
Collapse
Affiliation(s)
- Julien Troudet
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Régine Vignes-Lebbe
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Philippe Grandcolas
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Frédéric Legendre
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| |
Collapse
|
23
|
Boudinot BE. A general theory of genital homologies for the Hexapoda (Pancrustacea) derived from skeletomuscular correspondences, with emphasis on the Endopterygota. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:563-613. [PMID: 30419291 DOI: 10.1016/j.asd.2018.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
No consensus exists for the homology and terminology of the male genitalia of the Hexapoda despite over a century of debate. Based on dissections and the literature, genital skeletomusculature was compared across the Hexapoda and contrasted with the Remipedia, the closest pancrustacean outgroup. The pattern of origin and insertion for extrinsic and intrinsic genitalic musculature was found to be consistent among the Ectognatha, Protura, and the Remipedia, allowing for the inference of homologies given recent phylogenomic studies. The penis of the Hexapoda is inferred to be derived from medially-fused primary gonopods (gonopore-bearing limbs), while the genitalia of the Ectognatha are inferred to include both the tenth-segmental penis and the ninth-segmental secondary gonopods, similar to the genitalia of female insects which comprise gonopods of the eighth and ninth segments. A new nomenclatural system for hexapodan genitalic musculature is presented and applied, and a general list of anatomical concepts is provided. Novel and refined homologies are proposed for all hexapodan orders, and a series of groundplans are postulated. Emphasis is placed on the Endopterygota, for which fine-grained transition series are hypothesized given observed skeletomuscular correspondences.
Collapse
Affiliation(s)
- Brendon E Boudinot
- Department of Entomology & Nematology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA.
| |
Collapse
|
24
|
Collins RA, Hrbek T. An In Silico Comparison of Protocols for Dated Phylogenomics. Syst Biol 2018; 67:633-650. [PMID: 29319797 DOI: 10.1093/sysbio/syx089] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/24/2017] [Indexed: 01/02/2023] Open
Abstract
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clock models. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among the marker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems.
Collapse
Affiliation(s)
- Rupert A Collins
- Laboratório de Evolução e Genética Animal, Department of Genetics, Federal University of Amazonas, Av. Rodrigo Otavio Ramos, 3000, Manaus, AM, 69077-000, Brazil.,School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TH, UK
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Department of Genetics, Federal University of Amazonas, Av. Rodrigo Otavio Ramos, 3000, Manaus, AM, 69077-000, Brazil.,Department of Biology, 4102 LSB Brigham Young University, Provo, UT, 84602, USA
| |
Collapse
|
25
|
Billet G, Bardin J. Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals. Syst Biol 2018; 68:267-280. [DOI: 10.1093/sysbio/syy071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023] Open
Affiliation(s)
- Guillaume Billet
- CR2P, UMR 7207, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005 Paris, France
| | - Jérémie Bardin
- CR2P, UMR 7207, Sorbonne Université, MNHN, CNRS, T.46-56, E.5, case 104, 4 place Jussieu, 75252 Paris cedex 05, France
| |
Collapse
|
26
|
Abstract
Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.
Collapse
Affiliation(s)
- Scott Lidgard
- Integrative Research Center, Field Museum, Chicago, Illinois
| | - Alan C Love
- Department of Philosophy and the Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis
| |
Collapse
|
27
|
Penning DA. Quantitative axial myology in two constricting snakes: Lampropeltis holbrooki and Pantherophis obsoletus. J Anat 2018; 232:1016-1024. [PMID: 29484639 PMCID: PMC5979636 DOI: 10.1111/joa.12799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2018] [Indexed: 11/27/2022] Open
Abstract
A snake's body represents an extreme degree of elongation with immense muscle complexity. Snakes have approximately 25 different muscles on each side of the body at each vertebra. These muscles serially repeat, overlap, interconnect, and rarely insert parallel to the vertebral column. The angled muscles mean that simple measurements of anatomical cross-sectional area (ACSA, perpendicular to the long-axis of the body) serve only as proxies for the primary determinant of muscle force, physiological cross-sectional area (PCSA, area perpendicular to the muscle fibers). Here, I describe and quantify the musculature of two intraguild constrictors: kingsnakes (Lampropeltis holbrooki) and ratsnakes (Pantherophis obsoletus) whose predation performance varies considerably. Kingsnakes can produce significantly higher constriction pressures compared with ratsnakes of similar size. In both snakes, I provide qualitative descriptions, detail previously undescribed complexity, identify a new lateral muscle, and provide some of the first quantitative measures of individual muscle and whole-body PCSA. Furthermore, I compare measurements of ACSA with measurements of PCSA. There was no significant difference in PCSA of muscles between kingsnakes and ratsnakes. There is, however, a strong relationship between ACSA and PCSA measurements. I could not identify a significant difference in musculature between kingsnakes and ratsnakes that explains their different levels of constriction performance. Unmeasured components of muscle function, such as endurance and force production, might account for differences in performance between two species with similar muscle structure.
Collapse
Affiliation(s)
- David A. Penning
- Department of Biology & Environmental HealthMissouri Southern State UniversityJoplinMOUSA
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLAUSA
| |
Collapse
|
28
|
Vatanparast M, Powell A, Doyle JJ, Egan AN. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1036. [PMID: 29732266 PMCID: PMC5895186 DOI: 10.1002/aps3.1036] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/22/2018] [Indexed: 05/19/2023]
Abstract
PREMISE OF THE STUDY The development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts. METHODS Using 30 transcriptomes, we compared Hyb-Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation- and coalescent-based methods. RESULTS Hyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony-informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics. CONCLUSIONS Methods differed across criteria important for phylogenetic marker development. We recommend Hyb-Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community-driven efforts to reconstruct the legume tree of life.
Collapse
Affiliation(s)
- Mohammad Vatanparast
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionP.O. Box 37012, MRC 166WashingtonDC20560USA
- Present address:
Forest, Nature, and Biomass SectionDepartment of Geosciences and Natural Resource ManagementRolighedsvej 23, 1958 Frederiksberg C., University of CopenhagenDenmark
| | - Adrian Powell
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell University512 Mann LibraryIthacaNew York14853USA
- Present address:
Boyce Thompson Institute533 Tower RoadIthacaNew York14853USA
| | - Jeff J. Doyle
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell University512 Mann LibraryIthacaNew York14853USA
| | - Ashley N. Egan
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionP.O. Box 37012, MRC 166WashingtonDC20560USA
| |
Collapse
|
29
|
Pyron RA. Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians). Syst Biol 2018; 66:38-56. [PMID: 28173602 DOI: 10.1093/sysbio/syw068] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 02/04/2023] Open
Abstract
Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
Collapse
Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC, USA
| |
Collapse
|
30
|
Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods. Mol Phylogenet Evol 2018; 118:330-342. [DOI: 10.1016/j.ympev.2017.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022]
|
31
|
Lindenmayer DB, Likens GE, Franklin JF. Earth Observation Networks (EONs): Finding the Right Balance. Trends Ecol Evol 2017; 33:1-3. [PMID: 29103761 DOI: 10.1016/j.tree.2017.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 11/29/2022]
Abstract
Earth observation networks (EONs) are an emerging, surveillance-based approach to environmental monitoring and research that are fundamentally different than traditional question-driven, experimentally designed approaches. There is an urgent need to find an optimal balance between these approaches and to develop new integrated initiatives that take advantage of key features of them both.
Collapse
Affiliation(s)
- David B Lindenmayer
- Fenner School of Environment & Society, The Australian National University, Canberra, ACT 2601, Australia.
| | - Gene E Likens
- Cary Institute of Ecosystem Studies, Millbrook, NY 12545, USA; Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jerry F Franklin
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
32
|
Campbell MA, Alfaro ME, Belasco M, López JA. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ 2017; 5:e3548. [PMID: 28929008 PMCID: PMC5592902 DOI: 10.7717/peerj.3548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
Collapse
Affiliation(s)
- Matthew A Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of America
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Max Belasco
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - J Andrés López
- School of Fisheries and Ocean Sciencs, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,University of Alaska Museum, Fairbanks, AK, United States of America
| |
Collapse
|
33
|
Vicente Dos Santos V, Tixier MS. Which molecular markers for assessing which taxonomic level? The case study of the mite family Phytoseiidae (Acari: Mesostigmata). Cladistics 2017; 33:251-267. [PMID: 34715727 DOI: 10.1111/cla.12166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 11/29/2022] Open
Abstract
The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein-the predatory mite family Phytoseiidae-molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within-genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.
Collapse
Affiliation(s)
- Victor Vicente Dos Santos
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
| | - Marie-Stephane Tixier
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
| |
Collapse
|
34
|
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae). Mol Phylogenet Evol 2017; 107:345-355. [DOI: 10.1016/j.ympev.2016.11.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 11/19/2016] [Accepted: 11/27/2016] [Indexed: 11/17/2022]
|
35
|
Wipfler B, Pohl H, Yavorskaya MI, Beutel RG. A review of methods for analysing insect structures - the role of morphology in the age of phylogenomics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:60-68. [PMID: 27939712 DOI: 10.1016/j.cois.2016.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Techniques currently used in insect morphology are outlined briefly. Scanning electron microscopy (SEM) and microphotography are used mainly for documenting external features, the former providing more information on tiny surface structures and the latter on coloration, transparency and degree of sclerotization. A broad spectrum of methods is now available for anatomical studies: histological serial sections, confocal laser scanning microscopy (CLSM), light-sheet fluorescence microscopy (LSFM), serial block-face scanning electron microscopy (SBFSEM), dual beam scanning electron microscopy (FIB-SEM), nuclear magnetic resonance imaging (NMRI), and μ-computed tomography (micro-CT). The use of SBFSEM and FIB-SEM is restricted to extremely small samples. NMRI is used mainly in in vivo studies. Micro-computed tomography, in combination with computer-based reconstruction, has greatly accelerated the acquisition of high quality data in a phylogenetic context. Morphology will continue to play a vital role in phylogenetic and evolutionary investigations. It provides independent data for checking the plausibility of molecular phylogenies and is the only source of information for placing extinct taxa. It is the necessary basis for reconstructing character evolution on the phenotypic level and for developing complex evolutionary scenarios. Computer-based anatomical ontologies are an additional future perspective of morphological work.
Collapse
Affiliation(s)
- Benjamin Wipfler
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Hans Pohl
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Margarita I Yavorskaya
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Entomology Group, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany.
| |
Collapse
|
36
|
Zou Z, Zhang J. Morphological and molecular convergences in mammalian phylogenetics. Nat Commun 2016; 7:12758. [PMID: 27585543 PMCID: PMC5025827 DOI: 10.1038/ncomms12758] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/29/2016] [Indexed: 12/30/2022] Open
Abstract
Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference. Morphological characters are generally thought to have higher rates of convergence than molecular characters. Here, Zou and Zhang provide empirical evidence for this assumption and devise a method to improve the accuracy of phylogenetic reconstruction through identifying and removing convergence-prone characters.
Collapse
Affiliation(s)
- Zhengting Zou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
37
|
Fernández R, Edgecombe GD, Giribet G. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Syst Biol 2016; 65:871-89. [PMID: 27162151 PMCID: PMC4997009 DOI: 10.1093/sysbio/syw041] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/28/2016] [Indexed: 11/14/2022] Open
Abstract
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
Collapse
Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| |
Collapse
|
38
|
Lavoué S. Was Gondwanan breakup the cause of the intercontinental distribution of Osteoglossiformes? A time-calibrated phylogenetic test combining molecular, morphological, and paleontological evidence. Mol Phylogenet Evol 2016; 99:34-43. [DOI: 10.1016/j.ympev.2016.03.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 11/16/2022]
|
39
|
Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
|
40
|
Pyron RA, Hsieh FW, Lemmon AR, Lemmon EM, Hendry CR. Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12392] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Felisa W. Hsieh
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Alan R. Lemmon
- Department of Scientific Computing; Florida State University; Tallahassee FL 32306-4120 USA
| | - Emily M. Lemmon
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
| | - Catriona R. Hendry
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| |
Collapse
|
41
|
Smaers JB, Mongle CS, Kandler A. A multiple variance Brownian motion framework for estimating variable rates and inferring ancestral states. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12765] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeroen B. Smaers
- Department of Anthropology; Stony Brook University; Circle Rd, Stony Brook NY 11794-4364 USA
- Department of Anthropology; University College London; 14 Taviton Street London WC1H 0BW UK
- Research Department of Genetics; Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Carrie S. Mongle
- Department of Anthropology; Stony Brook University; Circle Rd, Stony Brook NY 11794-4364 USA
| | - Anne Kandler
- Department of Mathematics; City University London; Northampton Square; London EC1V 0HB UK
| |
Collapse
|
42
|
Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae). Mol Ecol Resour 2015; 16:1124-35. [DOI: 10.1111/1755-0998.12487] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
| | - Aaron Liston
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Vojtěch Zeisek
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| | - Kenneth Oberlander
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Kevin Weitemier
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Shannon C. K. Straub
- Department of Biology; Hobart and William Smith Colleges; 213 Eaton Hall Geneva NY 14456 USA
| | - Richard C. Cronn
- USDA Forest Service; Pacific Northwest Research Station; 3200 SW Jefferson Way Corvallis OR 97331 USA
| | - Léanne L. Dreyer
- Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Jan Suda
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| |
Collapse
|
43
|
Ruiz-Sanchez E. Parametric and non-parametric species delimitation methods result in the recognition of two new Neotropical woody bamboo species. Mol Phylogenet Evol 2015; 93:261-73. [DOI: 10.1016/j.ympev.2015.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 07/21/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
|
44
|
Heikkilä M, Mutanen M, Wahlberg N, Sihvonen P, Kaila L. Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol 2015; 15:260. [PMID: 26589618 PMCID: PMC4654798 DOI: 10.1186/s12862-015-0520-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. RESULTS Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. CONCLUSIONS The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
Collapse
Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, PO Box 3000, Oulu, 90014, Finland.
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, 20014, Finland.
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Pasi Sihvonen
- University of Helsinki, Research Affairs, PO Box 33, Helsinki, 00014, Finland.
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| |
Collapse
|
45
|
Affiliation(s)
- Sven Buerki
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | | |
Collapse
|
46
|
Schachat SR, Brown RL. Color Pattern on the Forewing of Micropterix (Lepidoptera: Micropterigidae): Insights into the Evolution of Wing Pattern and Wing Venation in Moths. PLoS One 2015; 10:e0139972. [PMID: 26437004 PMCID: PMC4593546 DOI: 10.1371/journal.pone.0139972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022] Open
Abstract
Wing patterns are key taxonomic characters that have long been used in descriptions of Lepidoptera; however, wing pattern homologies are not understood among different moth lineages. Here, we examine the relationship between wing venation and wing pattern in the genus Micropterix, among the most basal extant Lepidoptera, in order to evaluate the two existing predictive models that have the potential to establish wing pattern element homologies for the order. The location of wing pattern elements along the costal margin of the wing in Micropterix is consistent with the predictions of the model proposed for Tortricidae by Brown and Powell in 1991, later modified by Baixeras in 2002. The predictive power of this model for such distantly related taxa suggests that the model may hold across various superfamilies within Lepidoptera, and supports the long-held notion that fasciae, not spots, are the most likely primitive wing pattern elements for the order. In addition, the location of wing pattern elements suggests that the wing vein commonly termed Sc1 may in fact be a different vein, which Comstock identified in Trichoptera and referred to as "a."
Collapse
Affiliation(s)
- Sandra R. Schachat
- Mississippi Entomological Museum, Mississippi State, Mississippi, United States of America
- Department of Paleobiology, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Richard L. Brown
- Mississippi Entomological Museum, Mississippi State, Mississippi, United States of America
| |
Collapse
|
47
|
New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
48
|
Pyron RA. Advancing perspectives on parity-mode evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:562-3. [DOI: 10.1002/jez.b.22644] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/03/2023]
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences; The George Washington University; Washington District of Columbia
| |
Collapse
|