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Oliveira HFM, Freire-Jr GB, Silva DC, Mata VA, Abra FD, Camargo NFD, Araujo Goebel LG, Longo GR, Silva JM, Colli GR, Domingos FMCB. Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps. ENVIRONMENTAL RESEARCH 2024; 258:119374. [PMID: 38885824 DOI: 10.1016/j.envres.2024.119374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/11/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.
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Affiliation(s)
- Hernani Fernandes Magalhães Oliveira
- Departamento de Zoologia, Universidade Federal do Paraná - UFPR, Curitiba, Brazil; Departamento de Zoologia, Universidade de Brasília - UnB, Brasília, Brazil; Knowledge Center for Biodiversity, Belo Horizonte, MG, 31270-901, Brazil.
| | - Geraldo Brito Freire-Jr
- Departamento de Ecologia, Universidade de Brasília - UnB, Brasília, Brazil; Department of Biology, University of Nevada - UNR, Reno, USA
| | - Daiana Cardoso Silva
- Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso - UNEMAT, Nova Xavantina, Brazil
| | - Vanessa Alves Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Vila do Conde, Portugal
| | - Fernanda Delborgo Abra
- Smithsonian National Zoo and Conservation Biology Institute-Center for Conservation and Sustainability, Washington, DC, USA; ViaFAUNA Estudos Ambientais, São Paulo, SP, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | | | - L G Araujo Goebel
- Programa de Pós-graduação em Ciências Ambientais, Universidade do Estado de Mato Grosso - UNEMAT, Cáceres, Brazil
| | - Gabriela Rodrigues Longo
- Programa de Pós-graduação em Ensino de Ciências, Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, Brazil
| | - Joaquim Manoel Silva
- Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso - UNEMAT, Nova Xavantina, Brazil
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Arantes ÍC, Vasconcellos MM, Smith ML, Garrick RC, Colli GR, Noonan BP. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Mol Phylogenet Evol 2023:107843. [PMID: 37286064 DOI: 10.1016/j.ympev.2023.107843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.
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Affiliation(s)
- Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
| | - Mariana M Vasconcellos
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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3
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, Ahrens D. Standardized nuclear markers improve and homogenize species delimitation in Metazoa. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Paris‐Lodron‐University Salzburg Austria
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Sandra Kukowka
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Hannes Baur
- Naturhistorisches Museum Bern/Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Marianne Espeland
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Bernhard A. Huber
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Carl Hutter
- Museum of Natural Sciences and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Ximo Mengual
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Ralph S. Peters
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Miguel Vences
- Technische Universität Braunschweig Braunschweig Germany
| | - Thomas Wesener
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Keith Willmott
- Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert‐Ludwigs‐Universität Freiburg Freiburg im Breisgau Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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5
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dos Santos MV, Prudente ALC, Rodrigues MT, Sturaro MJ. The Role of Vicariance and Paleoclimatic Shifts in the Diversification of Uranoscodon superciliosus (Squamata, Tropiduridae) of the Amazonian Floodplains. Evol Biol 2022. [DOI: 10.1007/s11692-022-09583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Ishihara MA, Domingos FMCB, Gomides SC, Novelli IA, Colli GR, Vargas SM. Genetic structure of Enyalius capetinga (Squamata, Leiosauridae) in Central Cerrado and transitional areas between the Cerrado and the Atlantic forest, with updated geographic distribution. Genetica 2022; 150:367-377. [PMID: 36229707 DOI: 10.1007/s10709-022-00170-w] [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: 08/20/2021] [Accepted: 09/28/2022] [Indexed: 11/26/2022]
Abstract
The Brazilian Cerrado is considered a biodiversity hotspot highly threatened by human activities. Recently, many studies have demonstrated how underestimated is Cerrado's biodiversity considering squamate species, and the identification of divergent and cryptic lineages is essential for the formulation of effective conservation strategies. The transition areas between the Cerrado and the Atlantic Forest are even less known and, consequently, often dismissed in conservation policies. As previous studies suggested the presence of cryptic diversity within E. capetinga, we investigated patterns and processes in the geographic distribution of its genealogical lineages. We used DNA sequences from individuals collected in six localities and sequences publicly available from three mitochondrial markers (CYT-B, 16S and ND4) and one nuclear marker (C-Mos). We tested if the core and ecotone regions of the Cerrado show differences in biotic and abiotic characteristics that could promote genetic structure and divergence among lineages within E. capetinga. We found evidence for divergent lineages within the species, but not congruent with our hypothesis. Similar divergent patterns were observed in other Cerrado lizards, including interspecific divergences within the Enyalius genus. Molecular characterization of field-collected individuals (previously identified as E. bilineatus), allowed us to update the geographic distribution of the species to include the ecotone between the Cerrado and the Atlantic Forest, an area where species distribution overlap.
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Affiliation(s)
- M A Ishihara
- Departamento de Ciências Biológicas, Laboratório de Genética E Evolução Molecular, Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil.
- Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil.
| | - F M C B Domingos
- Departamento de Zoologia, Universidade Federal Do Paraná, Curitiba, PR, 81531-980, Brazil
| | - S C Gomides
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal do Oeste do Pará, Campus Oriximiná, Rodovia PA-254, 257, Oriximiná, PA, 68270-000, Brazil
| | - I A Novelli
- Laboratório de Zoologia, Centro Universitário de Lavras - UNILAVRAS, Lavras, MG, 37203-593, Brazil
| | - G R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - S M Vargas
- Departamento de Ciências Biológicas, Laboratório de Genética E Evolução Molecular, Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil
- Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil
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7
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Mittan CS, Zamudio KR, Thomé MTC, Camurugi F, Colli GR, Garda AA, Haddad CFB, Prado CPA. Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group. Mol Phylogenet Evol 2022; 175:107579. [PMID: 35835425 DOI: 10.1016/j.ympev.2022.107579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.
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Affiliation(s)
- Cinnamon S Mittan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - M Tereza C Thomé
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Cynthia P A Prado
- Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
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8
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Machado S, Hartwig Bessa M, Nornberg B, Silva Gottschalk M, Robe LJ. Unveiling the Mycodrosophila projectans (Diptera, Drosophilidae) species complex: Insights into the evolution of three Neotropical cryptic and syntopic species. PLoS One 2022; 17:e0268657. [PMID: 35613123 PMCID: PMC9132268 DOI: 10.1371/journal.pone.0268657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/04/2022] [Indexed: 11/22/2022] Open
Abstract
The Zygothrica genus group has been shown to be speciose, with a high number of cryptic species. DNA barcoding approaches have been a valuable tool to uncover cryptic diversity in this lineage, as recently suggested for the Neotropical Mycodrosophila projectans complex, which seems to comprise at least three different species. The aim of this study was to confirm the subdivision of the M. projectans complex while shedding some light on the patterns and processes related to its diversification. In this sense, the use of single and multi-locus datasets under phylogenetic, distance, coalescence, and diagnostic nucleotide approaches confirmed the presence of at least three species under the general morphotype previously described as M. projectans. Only a few subtle morphological differences were found for the three species in terms of aedeagus morphology and abdominal color patterns. Ecologically, sympatry and syntopy seem to be recurrent for these three cryptic species, which present widely overlapping niches, implying niche conservatism. This morphological and ecological similarity has persisted though cladogenesis within the complex, which dates back to the Miocene, providing an interesting example of morphological conservation despite ancient divergence. These results, in addition to contrasting patterns of past demographic fluctuations, allowed us to hypothesize patterns of allopatric or parapatric diversification with secondary contact in Southern Brazil. Nevertheless, genetic diversity was generally high within species, suggesting that migration may encompass an adaptive response to the restrictions imposed by the ephemerality of resources.
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Affiliation(s)
- Stela Machado
- Universidade Federal de Santa Maria (UFSM), Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Santa Maria, RS, Brazil
| | - Maiara Hartwig Bessa
- Universidade Federal de Santa Maria (UFSM), Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Santa Maria, RS, Brazil
| | - Bruna Nornberg
- Universidade Federal do Rio Grande (FURG), Instituto de Ciências Biológicas (ICB), Rio Grande, RS, Brasil
| | - Marco Silva Gottschalk
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas (UFPel), Instituto de Biologia, Campus Capão do Leão, Capão do Leão, RS, Brazil
| | - Lizandra Jaqueline Robe
- Universidade Federal de Santa Maria (UFSM), Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Santa Maria, RS, Brazil
- * E-mail:
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9
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Hancock ZB, Lehmberg ES, Blackmon H. Phylogenetics in Space: How Continuous Spatial Structure Impacts Tree Inference. Mol Phylogenet Evol 2022; 173:107505. [PMID: 35577296 DOI: 10.1016/j.ympev.2022.107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent - what we call the "missing z-axis". In this article, we review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. We illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. We find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by utilizing our results to suggest how researchers can identify spatial structure in phylogenetic datasets.
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10
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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11
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Hancock ZB, Blackmon H. Ghosts of a Structured Past: Impacts of Ancestral Patterns of Isolation-by-Distance on Divergence-Time Estimation. J Hered 2021; 111:573-582. [PMID: 33031560 PMCID: PMC7896184 DOI: 10.1093/jhered/esaa042] [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: 06/16/2020] [Indexed: 01/25/2023] Open
Abstract
Isolation-by-distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the population size. Next, we simulate whole genomes to obtain single nucleotide polymorphisms (SNPs), and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. Finally, we demonstrate the impact of ancestral isolation-by-distance on divergence-time estimation using an empirical dataset of squamates (Tropidurus) endemic to Brazil. We conclude that studies estimating divergence times should be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.
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Affiliation(s)
- Zachary B Hancock
- Department of Biology at Texas A&M University, College Station, TX.,Ecology & Evolutionary Biology Interdisciplinary Program at Texas A&M University, College Station, TX
| | - Heath Blackmon
- Department of Biology at Texas A&M University, College Station, TX.,Ecology & Evolutionary Biology Interdisciplinary Program at Texas A&M University, College Station, TX
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12
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Rossigalli-Costa N, Cury de Barros F, Cipriano AP, Prado Prandini L, Medeiros de Andrade T, Rothier PS, Lofeu L, Brandt R, Kohlsdorf T. A guide to incubate eggs of Tropidurus lizards under laboratory conditions. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:576-584. [PMID: 34496131 DOI: 10.1002/jez.b.23095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 01/11/2023]
Abstract
Studies in Evo-Devo benefit from the use of a variety of organisms, as comparative approaches provide a better understanding of Biodiversity and Evolution. Standardized protocols to incubate eggs and manipulate embryo development enable postulation of additional species as suitable biological systems for research in the field. In the past decades, vertebrate lineages such as Squamata (lizards, snakes, and amphisbaenians) emerged as crucial study systems for addressing topics as diverse as phenotypic evolution and climate change. However, protocols for maintaining gravid females and incubating eggs in the lab under experimental conditions are available to only a few squamate species. This resource article presents a simple incubation guide that standardizes conditions to maintain embryos of Tropidurus catalanensis (Squamata: Tropiduridae) under different experimental conditions, manipulating relevant environmental factors like temperature and humidity. We identified associated effects relating the egg incubation condition to developmental stage, incubation time, hatching success, and resulting morphotypes. Temperature and humidity play a key role in development and require attention when establishing the experimental design. Current literature comprises information for Tropidurus lizards that ponders how general in Squamata are the ecomorphs originally described for Anolis. Studies evaluating phenotypic effects of developmental environments suggest plasticity in some of the traits that characterize the ecomorphological associations described for this family. We expect that this incubation guide encourages future studies using Tropidurus lizards to address Evo-Devo questions.
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Affiliation(s)
- Nathalia Rossigalli-Costa
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | - Fábio Cury de Barros
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Department of Ecology and Evolutionary Biology, ICAQF, Federal University of São Paulo. Rua Prof. Artur Riedel, Diadema, Brazil.,University of the Estate of Minas Gerais (UEMG/Passos). Av. Juca Stockler 1130, Passos, Brazil
| | - Ana Paula Cipriano
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | - Luísa Prado Prandini
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | | | - Priscila S Rothier
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, 55 Rue Buffon, Paris, France
| | - Leandro Lofeu
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Renata Brandt
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Science North, Sudbury, Ontario, Canada
| | - Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
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13
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Kim D, Bauer BH, Near TJ. Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae). Syst Biol 2021; 71:273-285. [PMID: 33944950 DOI: 10.1093/sysbio/syab029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/14/2022] Open
Abstract
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Bruce H Bauer
- David A. Etnier Ichthyological Collection, 515 Hesler Biology Building, University of Tennessee, Knoxville, TN 37996, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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14
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Prado JRD, Knowles LL, Percequillo AR. New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America. Mol Phylogenet Evol 2020; 155:106992. [PMID: 33096231 DOI: 10.1016/j.ympev.2020.106992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/18/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
Taxa with broad geographic ranges that occur in different biomes and exhibit plastic morphological traits and/or adaptations to particular habitats make inferences about species boundaries especially challenging. However, technological and conceptual advances in the generation and analysis of genomic data have advanced the description of biodiversity. Here we address the outstanding questions about the delimitation of species in the genus Holochilus, a rodent with morphological specializations to wetland habitats distributed throughoutthe South America, using genome-wide SNP and morphometric data. Specifically, we apply a Bayesian model-based species delimitation that revealed significant re-arrangements of species boundaries based on consideration of both morphometric and genomic data alone, or in combination. With these shifts in species boundaries, our results provide an insightful framework for inferring the group's biogeographic history and considering possible connections between disjoint biomes in South America. Because of the ecological constraints of the marsh rats, and with the proposed taxonomic re-arrangements, the significance of our findings extends beyond systematics and suggests how diversification might be associated with past ecological/environmental changes during the Pleistocene. Overall, this study highlights how genomic data can provide phylogenetic information for resolving relationships among species of Holochilus, but also the importance of integrative approaches to identify evolutionary independent species. For the relatively understudied vast wetlands of South America, a robust species delimitation framework therefore becomes a critical source of data relevant to hypotheses about the history of the biomes themselves.
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Affiliation(s)
- Joyce Rodrigues do Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, Brazil.
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, Brazil
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15
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Liu T, Chen J, Jiang L, Qiao G. Phylogeny and species reassessment of
Hyalopterus
(Aphididae, Aphidinae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tongyi Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
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16
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Perea S, Sousa‐Santos C, Robalo J, Doadrio I. Multilocus phylogeny and systematics of Iberian endemicSqualius(Actinopterygii, Leuciscidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Perea
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales - CSIC Madrid Spain
| | - Carla Sousa‐Santos
- MARE – Marine and Environmental Sciences Centre ISPA‐Instituto Universitário Lisbon Portugal
| | - Joana Robalo
- MARE – Marine and Environmental Sciences Centre ISPA‐Instituto Universitário Lisbon Portugal
| | - Ignacio Doadrio
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales - CSIC Madrid Spain
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17
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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.
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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
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18
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Tonzo V, Papadopoulou A, Ortego J. Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex. Mol Ecol 2019; 28:3869-3886. [DOI: 10.1111/mec.15189] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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19
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko. Mol Phylogenet Evol 2019; 133:54-66. [DOI: 10.1016/j.ympev.2018.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022]
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20
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21
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Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches. Mol Phylogenet Evol 2019; 132:105-116. [DOI: 10.1016/j.ympev.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022]
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22
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Tekle YI, Wood FC. A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes. BMC Evol Biol 2018; 18:170. [PMID: 30445905 PMCID: PMC6240226 DOI: 10.1186/s12862-018-1283-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories. Conclusion Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1283-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fiona C Wood
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
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23
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Toussaint EFA, Breinholt JW, Earl C, Warren AD, Brower AVZ, Yago M, Dexter KM, Espeland M, Pierce NE, Lohman DJ, Kawahara AY. Anchored phylogenomics illuminates the skipper butterfly tree of life. BMC Evol Biol 2018; 18:101. [PMID: 29921227 PMCID: PMC6011192 DOI: 10.1186/s12862-018-1216-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/07/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. METHODS To infer a robust phylogenomic hypothesis for Hesperiidae, we sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers. Molecular datasets were analyzed using maximum-likelihood, parsimony and coalescent multi-species phylogenetic methods. RESULTS All analyses converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all nodes and all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as the sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within the grass skippers (Hesperiinae), there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a subfamily, are recovered as monophyletic with strong support, but are deeply nested within Hesperiinae. CONCLUSIONS Anchored Hybrid Enrichment sequencing resulted in a large amount of data that built the foundation for a new, robust evolutionary tree of skippers. The newly inferred phylogenetic tree resolves long-standing systematic issues and changes our understanding of the skipper tree of life. These resultsenhance understanding of the evolution of one of the most species-rich butterfly families.
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Affiliation(s)
- Emmanuel F A Toussaint
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- , RAPiD Genomics 747 SW 2nd Avenue IMB#14, Gainesville, FL, 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew D Warren
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew V Z Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Masaya Yago
- The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kelly M Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Marianne Espeland
- Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, 53113, Bonn, Germany
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, NY, 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, 10016, USA
- Entomology Section, National Museum of the Philippines, 1000, Manila, Philippines
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
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24
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Heckenhauer J, Samuel R, Ashton PS, Abu Salim K, Paun O. Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae (Dipterocarpaceae). Mol Phylogenet Evol 2018; 127:1-13. [PMID: 29778722 DOI: 10.1016/j.ympev.2018.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 10/16/2022]
Abstract
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae. Here, we develop a pipeline to maximize recovery of genome-wide SNPs from restriction-site associated DNA sequencing (RADseq) in non-model organisms across wide phylogenetic scales. We then infer phylogenomic relationships in the tribe Shoreeae using both traditional and coalescent analyses. The phylogenetic trees obtained with these methods are congruent to each other and highly resolved. They allow reconstructing the evolutionary patterns of floral traits (number of stamens, anther structure and anther/appendage size) in the group. Our inferences indicate that species with many stamens, but smaller, globose anthers and longer appendages and have evolved multiple times from species with fewer stamens, but larger, oblong anthers and shorter appendages. This could have happened in parallel to iterative shifts in pollinators across the uncovered phylogeny from larger, longer generation to smaller, shorter-generation insects that can quickly build up the necessary population sizes during mass flowering episodes.
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Affiliation(s)
- Jacqueline Heckenhauer
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria.
| | - Rosabelle Samuel
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
| | - Peter S Ashton
- Harvard University, Department of Organismic and Evolutionary Biology, 26 Oxford St, Cambridge, MA 02138, United States
| | - Kamariah Abu Salim
- University of Brunei Darussalam, Environmental and Life Sciences, Faculty of Science, Tungku Link Road, Gadong 1410, Brunei Darussalam
| | - Ovidiu Paun
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
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25
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Carvalho AL, Rivas LR, Céspedes R, Rodrigues MT. A New Collared Lizard (Tropidurus: Tropiduridae) Endemic to the Western Bolivian Andes and Its Implications for Seasonally Dry Tropical Forests. AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3896.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- André L.G. Carvalho
- Division of Vertebrate Zoology (Herpetology), American Museum of Natural History
- Richard Gilder Graduate School, American Museum of Natural History
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Luis Rolando Rivas
- Museo de Historia Natural Alcide d'Orbigny, Cochabamba, Bolivia
- Universidad Autónoma del Beni “Mcal. José Ballivián,” Trinidad, Beni, Bolivia
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26
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Zimmermann BL, Crivellaro MS, Hauschild CB, Bartholomei-Santos ML, Crandall KA, Pérez-Losada M, Giri F, Collins P, Santos S. Phylogeography reveals unexpectedly low genetic diversity in a widely distributed species: the case of the freshwater crab Aegla platensis (Decapoda: Anomura). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bianca L Zimmermann
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marcelo S Crivellaro
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Caroline B Hauschild
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Marlise L Bartholomei-Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Federico Giri
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Pablo Collins
- Laboratorio de Macrocrustáceos, Instituto Nacional de Limnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sandro Santos
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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27
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Heinicke MP, Lemmon AR, Lemmon EM, McGrath K, Hedges SB. Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). Mol Phylogenet Evol 2018; 118:145-155. [DOI: 10.1016/j.ympev.2017.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/15/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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28
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Wanke S, Granados Mendoza C, Müller S, Paizanni Guillén A, Neinhuis C, Lemmon AR, Lemmon EM, Samain MS. Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Mol Phylogenet Evol 2017; 117:111-123. [DOI: 10.1016/j.ympev.2017.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/05/2023]
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29
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Wang YH, Hsiao YW, Lee KH, Tseng HY, Lin YP, Komaki S, Lin SM. Acoustic differentiation and behavioral response reveals cryptic species within Buergeria treefrogs (Anura, Rhacophoridae) from Taiwan. PLoS One 2017; 12:e0184005. [PMID: 28877201 PMCID: PMC5587266 DOI: 10.1371/journal.pone.0184005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/16/2017] [Indexed: 11/30/2022] Open
Abstract
Buergeria japonica is a widely distributed treefrog occurring from Ryukyu Archipelago to Taiwan. Across this wide distributional range, we combined molecular, acoustic, morphological, and behavioral characters to clarify the taxonomic status among these insular populations. Genetic differentiation in mitochondrial sequences indicated an over 16% divergence among two deeply divergent clades: Japanese clade distributes in Ryukyu Archipelago and northwestern drainages of Taiwan, while Taiwanese clade distributes in the remaining drainages on Taiwan. The Taiwanese clade can be distinguished from the nominative species not only by molecular and morphological differences, but also distinguishable by considerable acoustic differentiation, which is extraordinarily noticeable for an additional type of long call that never recorded from Japanese clade. The two clades form a parapatric distribution pattern with narrow contact zones both in western and eastern Taiwan. Playback experiments indicated that male frogs show significantly stronger defensiveness against conspecific calls rather than heterospecific calls, indicating that these signals play a crucial role in species recognition. Here we describe the Taiwanese clade as a new species; the behavioral response and the magnitude of gene flow across their contact zones are especially worth for detailed studies.
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Affiliation(s)
- Ying-Han Wang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Wei Hsiao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ko-Huan Lee
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hui-Yun Tseng
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Yen-Po Lin
- Division of Zoology, Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - Shohei Komaki
- Division of Developmental Science, Graduate School for International Development and Cooperation, Hiroshima University, Hiroshima, Japan
- Global Career Design Center, Hiroshima University, Hiroshima, Japan
- * E-mail: (SK); (SML)
| | - Si-Min Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail: (SK); (SML)
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Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua). Mol Phylogenet Evol 2017; 111:65-75. [DOI: 10.1016/j.ympev.2017.03.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/14/2017] [Accepted: 03/23/2017] [Indexed: 01/08/2023]
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