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Rhodes JA, Baños H, Mitchell JD, Allman ES. MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. Bioinformatics 2021; 37:1766-1768. [PMID: 33031510 DOI: 10.1093/bioinformatics/btaa868] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/29/2022] Open
Abstract
SUMMARY MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.
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Affiliation(s)
- John A Rhodes
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA
| | - Hector Baños
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0160, USA
| | - Jonathan D Mitchell
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA.,Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - Elizabeth S Allman
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA
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152
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153
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Lu-Irving P, Bedoya AM, Salimena FRG, Dos Santos Silva TR, Viccini LF, Bitencourt C, Thode VA, Cardoso PH, O'Leary N, Olmstead RG. Phylogeny of Lantana, Lippia, and related genera (Lantaneae: Verbenaceae). AMERICAN JOURNAL OF BOTANY 2021; 108:1354-1373. [PMID: 34418063 DOI: 10.1002/ajb2.1708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Lantana and Lippia (Verbenaceae) are two large Linnean genera whose classification has been based on associated fruit traits: fleshy vs. dry fruits and one vs. two seed-bearing units. We reconstruct evolutionary relationships and the evolution of the two fruit traits to test the validity of these traits for classification. METHODS Previous studies of plastid DNA sequences provided limited resolution for this group. Consequently, seven nuclear loci, including ITS, ETS, and five PPR loci, were sequenced for 88 accessions of the Lantana/Lippia clade and three outgroups. RESULTS Neither Lantana nor Lippia is monophyletic. Burroughsia, Nashia, Phyla, and several Aloysia species are included within the clade comprising Lantana and Lippia. We provide a hypothesis for fruit evolution and biogeographic history in the group and their relevance for classification. CONCLUSIONS Fleshy fruits evolved multiple times in the Lantana/Lippia clade and thus are not suitable taxonomic characters. Several sections of Lantana and Lippia and the small genera are monophyletic, but Lippia section Zappania is broadly paraphyletic, making circumscription of genera difficult. Lippia sect. Rhodolippia is a polyphyletic group characterized by convergence in showy bracts. Species of Lantana sect. Sarcolippia, previously transferred to Lippia, are not monophyletic. The clade originated and diversified in South America, with at least four expansions into both Central America and the Caribbean and two to Africa. The types species of Lantana and Lippia occur in small sister clades, rendering any taxonomy that retains either genus similar to its current circumscription impossible.
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Affiliation(s)
- Patricia Lu-Irving
- Department of Biology, University of Washington, Washington, Seattle 98195, USA
| | - Ana M Bedoya
- Department of Biology, University of Washington, Washington, Seattle 98195, USA
| | - Fátima R G Salimena
- Departamento de Botânica, ICB, Universidade Federal de Juiz de Fora, CEP 36033-330, Juiz de Fora, Minas Gerais, Brazil
| | - Tânia R Dos Santos Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BR 116, CEP, Feira de Santana, Bahia 44031-460, Brazil
| | - Lyderson F Viccini
- Departamento de Botânica, ICB, Universidade Federal de Juiz de Fora, CEP 36033-330, Juiz de Fora, Minas Gerais, Brazil
| | - Cássia Bitencourt
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BR 116, CEP, Feira de Santana, Bahia 44031-460, Brazil
| | - Verônica A Thode
- Universidade Federal do Rio Grande do Sul, Departamento de Botânica, Programa de Pós-Graduação em Botânica, CEP, Porto Alegre, Rio Grande do Sul 91501-970, Brazil
| | - Pedro H Cardoso
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Botânica, Quinta da Boa Vista, CEP, Rio de Janeiro 20940-040, Brazil
| | - Nataly O'Leary
- Instituo de Botánica Darwinion, Labardén 200, cc 22, Buenos Aires, San Isidro B1642HYD, Argentina
| | - Richard G Olmstead
- Department of Biology, University of Washington, Washington, Seattle 98195, USA
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154
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Calixto-Rojas M, Lira-Noriega A, Rubio-Godoy M, Pérez-Ponce de León G, Pinacho-Pinacho CD. Phylogenetic relationships and ecological niche conservatism in killifish (Profundulidae) in Mesoamerica. JOURNAL OF FISH BIOLOGY 2021; 99:396-410. [PMID: 33733482 DOI: 10.1111/jfb.14727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 05/12/2023]
Abstract
The family Profundulidae is a group of small-sized fish species distributed between southern Mexico and Honduras, where they are frequently the only fish representatives at higher elevations in the basins where they occur. We characterized their ecological niche using different methods and metrics drawn from niche modelling and by re-examining phylogenetic relationships of a recently published molecular phylogeny of this family to gain a better understanding of its biogeographic and evolutionary history. We assessed both lines of evidence from the perspective of niche conservatism to set a foundation for discussing hypotheses about the processes underlying the distribution and evolution of the group. In fish clades where the species composition is not clear, we examined whether niche classification could be informative to discriminate groups geographically and ecologically consistent with any of the different hypotheses of valid species. The characterization of the ecological niche was carried out using the Maxent algorithm under different parameterizations and the projection of the presence on the main components of the most relevant environmental coverage, and the niche comparison was calculated with two indices (D and I), both in environmental space and in that projected geographically. With the molecular data, a species tree was generated using the *BEAST method. The comparison of these data was calculated with an age-overlap correlation test. Based on the molecular phylogeny and on niche overlap analyses, we uncovered strong evidence to support the idea that ecologically similar species are not necessarily sister species. The correlation analysis for genetic distance and niche overlap was not significant (P > 0.05). In clades with taxonomic conflicts, we only identified Profundulus oaxacae as a geographically and ecologically distinct group from P. punctatus. All the evidence considered leads us to propose that Profundulidae do not show evidence of niche conservatism and that there are reasons to consider P. oaxacae as a valid species. Our study suggests that niche divergence is a driving evolutionary force that caused the diversification and speciation processes of the Profundulidae, along with the geological and climatic events that promoted the expansion or contraction of suitable environments.
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Affiliation(s)
- Miguel Calixto-Rojas
- Doctorado en Ciencias, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, Veracruz, Mexico
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Instituto de Ecología A. C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, Veracruz, Mexico
| | - Miguel Rubio-Godoy
- Instituto de Ecología, A.C., Red de Biología Evolutiva, Carretera Antigua a Coatepec 351, Veracruz, Mexico
| | | | - Carlos D Pinacho-Pinacho
- CONACyT Research Fellow, Instituto de Ecología A. C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, Veracruz, Mexico
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155
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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156
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Viñuela Rodríguez N, Šanda R, Zogaris S, Vukić J. Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula. Mol Phylogenet Evol 2021; 164:107274. [PMID: 34333114 DOI: 10.1016/j.ympev.2021.107274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.
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Affiliation(s)
- Nuria Viñuela Rodríguez
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic; Department of Zoology, National Museum, Václavské nám. 68, Prague 1, 11000, Czech Republic
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Sciences and Inland Waters, Athinon-Souniou Ave., Anavissos, Attica, 19013, Greece
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic.
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157
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MacGuigan DJ, Hoagstrom CW, Domisch S, Hulsey CD, Near TJ. Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Sami Domisch
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - C. Darrin Hulsey
- Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Peabody Museum of Natural History Yale University New Haven CT USA
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158
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Rhodes JA, Baños H, Mitchell JD, Allman ES. MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. BIOINFORMATICS (OXFORD, ENGLAND) 2021; 37:1766-1768. [PMID: 33031510 DOI: 10.1101/2020.05.01.073361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 05/26/2023]
Abstract
SUMMARY MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.
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Affiliation(s)
- John A Rhodes
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA
| | - Hector Baños
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0160, USA
| | - Jonathan D Mitchell
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - Elizabeth S Allman
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99775-6660, USA
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159
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Maggioni D, Garese A, Huang D, Hoeksema BW, Arrigoni R, Seveso D, Galli P, Berumen ML, Montalbetti E, Pica D, Torsani F, Montano S. Diversity, host specificity and biogeography in the Cladocorynidae (Hydrozoa, Capitata), with description of a new genus. Cladistics 2021; 38:13-37. [DOI: 10.1111/cla.12480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Davide Maggioni
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Agustín Garese
- Instituto de Investigaciones Marinas y Costeras (IIMyC) Facultad de Ciencias Exactas y Naturales Universidad Nacional de Mar del Plata (UNMDP) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Mar del Plata 7600 Argentina
| | - Danwei Huang
- Department of Biological Sciences Tropical Marine Science Institute and Centre for Nature‐based Climate Solutions National University of Singapore Singapore 117558 Singapore
| | - Bert W. Hoeksema
- Taxonomy, Systematics and Geodiversity Group Naturalis Biodiversity Center Leiden 2300 RA The Netherlands
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen 9700 CC The Netherlands
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM) Stazione Zoologica Anton Dohrn Villa Comunale Napoli 80121 Italy
| | - Davide Seveso
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Paolo Galli
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955‐6900 Saudi Arabia
| | - Enrico Montalbetti
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Daniela Pica
- Department of Biological and Environmental Sciences and Technologies University of Salento Lecce 73100 Italy
- CoNISMa – Consorzio Nazionale Interuniversitario per le Scienze del Mare Roma 00196 Italy
| | - Fabrizio Torsani
- Department of Life and Environmental Sciences Polytechnic University of Marche Ancona 60131 Italy
| | - Simone Montano
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
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160
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Torres A, Goloboff PA, Catalano SA. Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology). Cladistics 2021; 38:103-125. [DOI: 10.1111/cla.12477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
| | - Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- American Museum of Natural History 200 Central Park West New York NY 10024 USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 S. M. de Tucumán Tucumán 4000 Argentina
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161
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Beltrán-López RG, Pérez-Rodríguez R, Montañez-García OC, Artigas-Azas JM, Köck M, Mar-Silva AF, Domínguez-Domínguez O. Genetic differentiation in the genus Characodon: implications for conservation and taxonomy. PeerJ 2021; 9:e11492. [PMID: 34285828 PMCID: PMC8272924 DOI: 10.7717/peerj.11492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.
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Affiliation(s)
- Rosa G Beltrán-López
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.,Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Ofelia C Montañez-García
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | | | | | - Adán F Mar-Silva
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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162
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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163
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Kozak KM, Joron M, McMillan WO, Jiggins CD. Rampant Genome-Wide Admixture across the Heliconius Radiation. Genome Biol Evol 2021; 13:evab099. [PMID: 33944917 PMCID: PMC8283734 DOI: 10.1093/gbe/evab099] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.
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Affiliation(s)
- Krzysztof M Kozak
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| | - Mathieu Joron
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, France
| | | | - Chris D Jiggins
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
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164
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Ogilvie HA, Mendes FK, Vaughan TG, Matzke NJ, Stadler T, Welch D, Drummond AJ. Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales. Syst Biol 2021; 71:208-220. [PMID: 34228807 PMCID: PMC8677526 DOI: 10.1093/sysbio/syab054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth–death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth–death; molecular clock; multispecies coalescent; phylogenetics; species trees.]
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Affiliation(s)
- Huw A Ogilvie
- Department of Computer Science, Rice University, Houston TX, 77005, USA
| | - Fábio K Mendes
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Nicholas J Matzke
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, 4058, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - David Welch
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland, 1010, New Zealand.,School of Computer Science, The University of Auckland, Auckland, 1010, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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165
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Vázquez-Miranda H, Barker FK. Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus. Mol Phylogenet Evol 2021; 163:107242. [PMID: 34224849 DOI: 10.1016/j.ympev.2021.107242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 01/18/2023]
Abstract
Although there is general consensus that sampling of multiple genetic loci is critical in accurate reconstruction of species trees, the exact numbers and the best types of molecular markers remain an open question. In particular, the phylogenetic utility of sex-linked loci is underexplored. Here, we sample all species and 70% of the named diversity of the New World wren genus Campylorhynchus using sequences from 23 loci, to evaluate the effects of linkage on efficiency in recovering a well-supported tree for the group. At a tree-wide level, we found that most loci supported fewer than half the possible clades and that sex-linked loci produced similar resolution to slower-coalescing autosomal markers, controlling for locus length. By contrast, we did find evidence that linkage affected the efficiency of recovery of individual relationships; as few as two sex-linked loci were necessary to resolve a selection of clades with long to medium subtending branches, whereas 4-6 autosomal loci were necessary to achieve comparable results. These results support an expanded role for sampling of the avian Z chromosome in phylogenetic studies, including target enrichment approaches. Our concatenated and species tree analyses represent significant improvements in our understanding of diversification in Campylorhynchus, and suggest a relatively complex scenario for its radiation across the Miocene/Pliocene boundary, with multiple invasions of South America.
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Affiliation(s)
- Hernán Vázquez-Miranda
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, Bell Museum of Natural History, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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166
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Thomas AE, Igea J, Meudt HM, Albach DC, Lee WG, Tanentzap AJ. Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. AMERICAN JOURNAL OF BOTANY 2021; 108:1289-1306. [PMID: 34173225 DOI: 10.1002/ajb2.1678] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations. METHODS Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species. RESULTS We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation. CONCLUSIONS Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.
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Affiliation(s)
- Anne E Thomas
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Javier Igea
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Heidi M Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Dirk C Albach
- Carl von Ossietzky-University, Oldenburg, D-26111, Germany
| | - William G Lee
- Manaaki Whenua - Landcare Research Otago, Dunedin, New Zealand
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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167
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Chumová Z, Záveská E, Hloušková P, Ponert J, Schmidt PA, Čertner M, Mandáková T, Trávníček P. Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:511-524. [PMID: 33960537 DOI: 10.1111/tpj.15306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 05/21/2023]
Abstract
Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, University of Innsbruck, Sternwartestraße 15, Innsbruck, 6020, Austria
| | | | - Jan Ponert
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Philipp-André Schmidt
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
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168
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. AMERICAN JOURNAL OF BOTANY 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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169
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Vite-Garín T, Estrada-Bárcenas DA, Gernandt DS, Reyes-Montes MDR, Sahaza JH, Canteros CE, Ramírez JA, Rodríguez-Arellanes G, Serra-Damasceno L, Zancopé-Oliveira RM, Taylor JW, Taylor ML. Histoplasma capsulatum Isolated from Tadarida brasiliensis Bats Captured in Mexico Form a Sister Group to North American Class 2 Clade. J Fungi (Basel) 2021; 7:529. [PMID: 34209122 PMCID: PMC8305335 DOI: 10.3390/jof7070529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 01/11/2023] Open
Abstract
Histoplasma capsulatum is a dimorphic fungus associated with respiratory and systemic infections in mammalian hosts that have inhaled infective mycelial propagules. A phylogenetic reconstruction of this pathogen, using partial sequences of arf, H-anti, ole1, and tub1 protein-coding genes, proposed that H. capsulatum has at least 11 phylogenetic species, highlighting a clade (BAC1) comprising three H. capsulatum isolates from infected bats captured in Mexico. Here, relationships for each individual locus and the concatenated coding regions of these genes were inferred using parsimony, maximum likelihood, and Bayesian inference methods. Coalescent-based analyses, a concatenated sequence-types (CSTs) network, and nucleotide diversities were also evaluated. The results suggest that six H. capsulatum isolates from the migratory bat Tadarida brasiliensis together with one isolate from a Mormoops megalophylla bat support a NAm 3 clade, replacing the formerly reported BAC1 clade. In addition, three H. capsulatum isolates from T. brasiliensis were classified as lineages. The concatenated sequence analyses and the CSTs network validate these findings, suggesting that NAm 3 is related to the North American class 2 clade and that both clades could share a recent common ancestor. Our results provide original information on the geographic distribution, genetic diversity, and host specificity of H. capsulatum.
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Affiliation(s)
- Tania Vite-Garín
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Daniel A. Estrada-Bárcenas
- Colección Nacional de Cepas Microbianas y Cultivos Celulares, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV, IPN), Ciudad de México 07360, Mexico;
| | - David S. Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico;
| | - María del Rocío Reyes-Montes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Jorge H. Sahaza
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Cristina E. Canteros
- Departamento de Micología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires 1281, Argentina;
| | - José A. Ramírez
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Gabriela Rodríguez-Arellanes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Lisandra Serra-Damasceno
- Centro de Ciências da Saúde, Departamento de Saúde Comunitária, Universidade Federal do Ceará, Fortaleza 60455-610, Brazil;
| | - Rosely M. Zancopé-Oliveira
- Laboratório de Micologia, Setor Imunodiagnóstico, Instituto Nacional de Infectología Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil;
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA;
| | - Maria Lucia Taylor
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
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170
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Quintero-Galvis JF, Saenz-Agudelo P, Celis-Diez JL, Amico GC, Vazquez S, Shafer ABA, Nespolo RF. The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus. Mol Phylogenet Evol 2021; 163:107234. [PMID: 34146676 DOI: 10.1016/j.ympev.2021.107234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 01/16/2023]
Abstract
The current distribution of the flora and fauna of southern South America is the result of drastic geological events that occurred during the last 20 million years, including marine transgressions, glaciations and active vulcanism. All these have been associated with fragmentation, isolation and subsequent expansion of the biota, south of 35°S, such as the temperate rainforest. This forest is mostly dominated by Nothofagus trees and is the habitat of the relict marsupial monito del monte, genus Dromiciops, sole survivor of the order Microbiotheria. Preliminary analyses using mtDNA proposed the existence of three main Dromiciops lineages, distributed latitudinally, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocene) biogeographic history for the genus. We performed phylogenetic reconstructions using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens from 31 sites across Chile and Argentina. Our phylogenetic analysis resolved three main clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which should be considered a distinct species (D. bozinovici, sensu D'Elía et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about ~13 million years ago. Divergence time estimates for the southern clades (39.6°S to 42.0°S) ranged from 9.57 to 6.5 Mya. A strong genetic structure was also detected within and between clades. Demographic analyses suggest population size stability for the northern clade (D. bozinovici), and recent demographic expansions for the central and southern clades. All together, our results suggest that the diversification of Dromiciops were initiated by the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of Los Andes between 37 and 48°S. The MMT resulted from an increase in global sea levels at the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat of Dromiciops.
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Affiliation(s)
- Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan L Celis-Diez
- Pontificia Universidad Católica de Valparaíso Escuela de Agronomía Quillota, Chile
| | - Guillermo C Amico
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Soledad Vazquez
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Aaron B A Shafer
- Department of Forensic Science & Environmental Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
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171
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Abstract
The Antarctic environment is famously inhospitable to most terrestrial biodiversity, traditionally viewed as a driver of species extinction. Combining population- and species-level molecular data, we show that beetles on islands along the Antarctic Polar Front diversified in response to major climatic events over the last 50 Ma in surprising synchrony with the region’s marine organisms. Unique algae- and moss-feeding habits enabled beetles to capitalize on cooling conditions, which resulted in a decline in flowering plants—the typical hosts for beetles elsewhere. Antarctica’s cooling paleoclimate thus fostered the diversification of both terrestrial and marine life. Climatically driven evolutionary processes since the Miocene may underpin much of the region’s diversity, are still ongoing, and should be further investigated among Antarctic biota. Global cooling and glacial–interglacial cycles since Antarctica’s isolation have been responsible for the diversification of the region’s marine fauna. By contrast, these same Earth system processes are thought to have played little role terrestrially, other than driving widespread extinctions. Here, we show that on islands along the Antarctic Polar Front, paleoclimatic processes have been key to diversification of one of the world’s most geographically isolated and unique groups of herbivorous beetles—Ectemnorhinini weevils. Combining phylogenomic, phylogenetic, and phylogeographic approaches, we demonstrate that these weevils colonized the sub-Antarctic islands from Africa at least 50 Ma ago and repeatedly dispersed among them. As the climate cooled from the mid-Miocene, diversification of the beetles accelerated, resulting in two species-rich clades. One of these clades specialized to feed on cryptogams, typical of the polar habitats that came to prevail under Miocene conditions yet remarkable as a food source for any beetle. This clade’s most unusual representative is a marine weevil currently undergoing further speciation. The other clade retained the more common weevil habit of feeding on angiosperms, which likely survived glaciation in isolated refugia. Diversification of Ectemnorhinini weevils occurred in synchrony with many other Antarctic radiations, including penguins and notothenioid fishes, and coincided with major environmental changes. Our results thus indicate that geo-climatically driven diversification has progressed similarly for Antarctic marine and terrestrial organisms since the Miocene, potentially constituting a general biodiversity paradigm that should be sought broadly for the region’s taxa.
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172
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Mahbub M, Wahab Z, Reaz R, Rahman MS, Bayzid MS. wQFM: Highly Accurate Genome-scale Species Tree Estimation from Weighted Quartets. Bioinformatics 2021; 37:3734-3743. [PMID: 34086858 DOI: 10.1093/bioinformatics/btab428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. RESULTS We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL. AVAILABILITY wQFM is available in open source form at https://github.com/Mahim1997/wQFM-2020. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mahim Mahbub
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Zahin Wahab
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - M Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
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173
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Guimarães RR, Rocha RG, Loss AC, Mendes-Oliveira AC, Patterson BD, Costa LP. Morphological and molecular discordance in the taxonomic rearrangement of the Marmosops pinheiroi complex (Marsupialia: Didelphidae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1921877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Roger Rodrigues Guimarães
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
| | - Rita Gomes Rocha
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Ana Carolina Loss
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
- National Institute of the Atlantic Forest, Av. José Ruschi, 4, Santa Teresa, 29650-000, ES, Brazil
| | | | - Bruce D. Patterson
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, 60605, IL, USA
| | - Leonora Pires Costa
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
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174
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Castro-Pereira D, Peres EA, Pinto-da-Rocha R. Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmen Neosadocus Mello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae). PLoS One 2021; 16:e0249746. [PMID: 34077418 PMCID: PMC8171921 DOI: 10.1371/journal.pone.0249746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 11/26/2022] Open
Abstract
Neosadocus harvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution about Neosadocus includes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species' diversity in a phylogeographical framework. Our results show that Neosadocus is a monophyletic group and comprises four species: N. bufo, N. maximus, N. robustus and N. misandrus (which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism in N. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work: "Bunoweyhia" variabilis Mello-Leitão, 1935 = Neosadocus bufo (Mello-Leitão, 1926); and "Bunoweyhia" minor Mello-Leitão, 1935 = Neosadocus maximus (Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.
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Affiliation(s)
- Daniel Castro-Pereira
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Elen A. Peres
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ricardo Pinto-da-Rocha
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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175
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Sklenář F, Jurjević Ž, Houbraken J, Kolařík M, Arendrup M, Jørgensen K, Siqueira J, Gené J, Yaguchi T, Ezekiel C, Silva Pereira C, Hubka V. Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species. Stud Mycol 2021; 99:100120. [PMID: 35003383 PMCID: PMC8688885 DOI: 10.1016/j.simyco.2021.100120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. A. alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A. capensis is synonymized with A. iizukae. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section Flavipedes species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for A. fumigatus wild-type were found for both triazoles and amphotericin B for A. ardalensis, A. iizukae, and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae and A. suttoniae were comparable to or more susceptible as A. fumigatus. Finally, terbinafine was in vitro active against all species except A. alboviridis.
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Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - M. Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - M.C. Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - K.M. Jørgensen
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - J.P.Z. Siqueira
- Laboratório de Microbiologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - C. Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
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176
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Brusa JL, Rotella JJ, Banner KM, Hutchins PR. Challenges and opportunities for comparative studies of survival rates: An example with male pinnipeds. Ecol Evol 2021; 11:7980-7999. [PMID: 34188866 PMCID: PMC8216918 DOI: 10.1002/ece3.7627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/11/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
Survival rates are a central component of life-history strategies of large vertebrate species. However, comparative studies seldom investigate interspecific variation in survival rates with respect to other life-history traits, especially for males. The lack of such studies could be due to the challenges associated with obtaining reliable datasets, incorporating information on the 0-1 probability scale, or dealing with several types of measurement error in life-history traits, which can be a computationally intensive process that is often absent in comparative studies. We present a quantitative approach using a Bayesian phylogenetically controlled regression with the flexibility to incorporate uncertainty in estimated survival rates and quantitative life-history traits while considering genetic similarity among species and uncertainty in relatedness. As with any comparative analysis, our approach makes several assumptions regarding the generalizability and comparability of empirical data from separate studies. Our model is versatile in that it can be applied to any species group of interest and include any life-history traits as covariates. We used an unbiased simulation framework to provide "proof of concept" for our model and applied a slightly richer model to a real data example for pinnipeds. Pinnipeds are an excellent taxonomic group for comparative analysis, but survival rate data are scarce. Our work elucidates the challenges associated with addressing important questions related to broader ecological life-history patterns and how survival-reproduction trade-offs might shape evolutionary histories of extant taxa. Specifically, we underscore the importance of having high-quality estimates of age-specific survival rates and information on other life-history traits that reasonably characterize a species for accurately comparing across species.
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Affiliation(s)
- Jamie L. Brusa
- Department of EcologyMontana State UniversityBozemanMTUSA
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWAUSA
| | - Jay J. Rotella
- Department of EcologyMontana State UniversityBozemanMTUSA
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177
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Shen CZ, Zhang CJ, Chen J, Guo YP. Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae). FRONTIERS IN PLANT SCIENCE 2021; 12:648026. [PMID: 34122473 PMCID: PMC8187803 DOI: 10.3389/fpls.2021.648026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/20/2021] [Indexed: 05/12/2023]
Abstract
Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.
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Affiliation(s)
- Chu-Ze Shen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chu-Jie Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Jie Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yan-Ping Guo
- School of Life Sciences, Peking University, Beijing, China
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178
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Dismukes W, Heath TA. treeducken: An R package for simulating cophylogenetic systems. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wade Dismukes
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USA
| | - Tracy A. Heath
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USA
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179
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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180
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Lax P, Gonzalez‐Ittig RE, Rondan Dueñas JC, Andrade AJ, Gardenal CN, Franco J, Doucet ME. Decrypting species in the
Nacobbus aberrans
(Nematoda: Pratylenchidae) complex using integrative taxonomy. ZOOL SCR 2021. [DOI: 10.1111/zsc.12494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Paola Lax
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Raúl E. Gonzalez‐Ittig
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Juan C. Rondan Dueñas
- Laboratorio de Biología Molecular Pabellón CEPROCOR Santa María de Punilla Córdoba, Argentina
| | - Alberto J. Andrade
- Instituto de Biología de la Altura Universidad Nacional de Jujuy San Salvador de Jujuy Argentina
| | - Cristina N. Gardenal
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | | | - Marcelo E. Doucet
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
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181
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de Paula AS, Barreto C, Telmo MCM, Diotaiuti L, Galvão C. Historical Biogeography and the Evolution of Hematophagy in Rhodniini (Heteroptera: Reduviidae: Triatominae). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.660151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Rhodniini tribe is one of the five tribes in the subfamily Triatominae and is notorious for its domestic blood-sucking pests and vectors of Trypanosoma cruzi across Latin America. The human and economic costs of the Chagas disease in the American tropics are considerable, and these insects are of unquestionable importance to humans. We used mitochondrial rDNA (16S), nuclear ribosomal RNA (28S) and wingless (Wg) sequences to perform phylogenetic analysis to derive trees based on parsimony and maximum likelihood. Nucleotide sequences were used in molecular-clock analyses to estimate time divergence between species of Rhodniini. The potential distribution of each species was modeled and compared with Kappa statistic. Multivariate niches with bioclimatic variables were used to describe differences between the species using discriminant analysis. The results of this study indicate that the Rhodniini originated 17.91 Mya ago. Rhodnius domesticus is the oldest species having its origin at 9.13 Mya. Rhodniini are closely related to Salyavatinae that are specialist termite predators and diverged from this subfamily 30.43 Mya. Most species are clearly allopatric and have distinct bioclimatic niches. The colonization of bromeliads, palms trees and bird nests represent important events for the speciation of these taxa. The hematophagous habit can be described as a scenario where Rhodniini’s ancestor could be pre-adapted for the invasion of bromeliads, palm trees, and bird nests where they would find significant water availability and thermal damping. These environments are widely used by vertebrate inquilines that would be the source of food for the species of Rhodniini. Lastly, our results show an alternative position of Psammolestes in the phylogenetic tree.
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182
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Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
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Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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183
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Munds RA, Titus CL, Moreira LAA, Eggert LS, Blomquist GE. Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae). Ecol Evol 2021; 11:4442-4459. [PMID: 33976821 PMCID: PMC8093732 DOI: 10.1002/ece3.7338] [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: 05/16/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023] Open
Abstract
Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
- Nocturnal Primate Research GroupOxford Brookes UniversityOxfordUK
| | - Chelsea L. Titus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Lais A. A. Moreira
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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184
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He K, Eastman TG, Czolacz H, Li S, Shinohara A, Kawada SI, Springer MS, Berenbrink M, Campbell KL. Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers. eLife 2021; 10:e66797. [PMID: 33949308 PMCID: PMC8205494 DOI: 10.7554/elife.66797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
The speciose mammalian order Eulipotyphla (moles, shrews, hedgehogs, solenodons) combines an unusual diversity of semi-aquatic, semi-fossorial, and fossorial forms that arose from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these lifestyles has been confounded by a fragmentary fossil record, unresolved phylogenetic relationships, and potential morphological convergence, calling for novel approaches. The net surface charge of the oxygen-storing muscle protein myoglobin (ZMb), which can be readily determined from its primary structure, provides an objective target to address this question due to mechanistic linkages with myoglobin concentration. Here, we generate a comprehensive 71 species molecular phylogeny that resolves previously intractable intra-family relationships and then ancestrally reconstruct ZMb evolution to identify ancient lifestyle transitions based on protein sequence alone. Our phylogenetically informed analyses confidently resolve fossorial habits having evolved twice in talpid moles and reveal five independent secondary aquatic transitions in the order housing the world's smallest endothermic divers.
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Affiliation(s)
- Kai He
- Department of Biological Sciences, University of ManitobaWinnipegCanada
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical UniversityGuangzhouChina
| | - Triston G Eastman
- Department of Biological Sciences, University of ManitobaWinnipegCanada
| | - Hannah Czolacz
- Department of Evolution, Ecology and Behaviour, University of LiverpoolLiverpoolUnited Kingdom
| | - Shuhao Li
- Department of Biological Sciences, University of ManitobaWinnipegCanada
| | - Akio Shinohara
- Department of Bio-resources, Division of Biotechnology, Frontier Science Research Center, University of MiyazakiMiyazakiJapan
| | - Shin-ichiro Kawada
- Department of Zoology, Division of Vertebrates, National Museum of Nature and ScienceTokyoJapan
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, RiversideRiversideUnited States
| | - Michael Berenbrink
- Department of Evolution, Ecology and Behaviour, University of LiverpoolLiverpoolUnited Kingdom
| | - Kevin L Campbell
- Department of Biological Sciences, University of ManitobaWinnipegCanada
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185
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Douglas J. UglyTrees: a browser-based multispecies coalescent tree visualizer. Bioinformatics 2021; 37:268-269. [PMID: 32717041 PMCID: PMC8055222 DOI: 10.1093/bioinformatics/btaa679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 01/20/2023] Open
Abstract
SUMMARY Visualization is a vital task in phylogenetics and yet there is a deficit in programs which visualize the multispecies coalescent (MSC) model. UglyTrees (UT) is an easy-to-use program for visualizing multiple gene trees embedded within a single species trees. The mapping between gene and species nodes is automatically detected allowing for ready access to the program. UT can scrape the contents of a website for MSC analyses, enabling the sharing of interactive MSC figures through optional parameters in the URL. If a posterior distribution is uploaded, the transitions between MSC states are animated allowing the visual tracking of trees throughout the sequence. AVAILABILITY AND IMPLEMENTATION UT runs in all major web browsers including mobile devices, and is hosted at www.uglytrees.nz. The MIT-licensed code is available at https://github.com/UglyTrees/uglytrees.github.io.
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Affiliation(s)
- Jordan Douglas
- School of Computer Science, University of Auckland, Auckland 1010, New Zealand
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186
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Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA. Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 2021; 9:e11310. [PMID: 33981506 PMCID: PMC8074845 DOI: 10.7717/peerj.11310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
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Affiliation(s)
- Petr G. Garibian
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I.D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Anna N. Neretina
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, New York, United States
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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187
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Abstract
Abstract
The genus Oligoryzomys is the most speciose genus in the tribe Oryzomyini; however, under the general lineage concept of species, at least nine lineages are pending review and naming. In this study, I carry out qualitative and quantitative morphological analyses of specimens of Oligoryzomys andinus, O. aff. andinus, and O. arenalis, to delimit these three lineages. I show that O. aff. andinus is morphologically distinct both from O. andinus and O. arenalis, corroborating that the lineage merits recognition as a species, as suggested by previously published molecular analyses (Hurtado and D’Elía 2019). I therefore describe O. aff. andinus as a new species endemic to the Polylepis forests on the western slope of the Andes and coastal Lomas in central Peru. Finally, I propose two hypotheses about the biogeographical history of O. andinus, O. arenalis, and this new species.
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Affiliation(s)
- Natali Hurtado
- Universidad Nacional de San Agustín de Arequipa, Calle Santa Catalina 117, postal code 04001, Arequipa, PE, Peru
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188
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Farah IT, Islam MM, Zinat KT, Rahman AH, Bayzid MS. Species tree estimation from gene trees by minimizing deep coalescence and maximizing quartet consistency: a comparative study and the presence of pseudo species tree terraces. Syst Biol 2021; 70:1213-1231. [PMID: 33844023 DOI: 10.1093/sysbio/syab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022] Open
Abstract
Species tree estimation from multi-locus datasets is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by "summarizing" a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e., quartet score, extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multi-locus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. We present a comprehensive comparative study of these two optimality criteria. Our experiments, on a collection of datasets simulated under ILS, indicate that MDC may result in competitive or identical quartet consistency score as MQC, but could be significantly worse than MQC in terms of tree accuracy - demonstrating the presence and impacts of equally optimal species trees. This is the first known study that provides the conditions for the datasets to have equally optimal trees in the context of phylogenomic inference using summary methods.
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Affiliation(s)
- Ishrat Tanzila Farah
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
| | - Md Muktadirul Islam
- Applied Statistics and Data Science (ASDS), Department of Statistics Jahangirnagar University Dhaka-1342, Bangladesh
| | - Kazi Tasnim Zinat
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh.,Department of Computer Science University of Maryland, College Park, Maryland, USA
| | - Atif Hasan Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
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189
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Abad-Franch F, Monteiro FA, Pavan MG, Patterson JS, Bargues MD, Zuriaga MÁ, Aguilar M, Beard CB, Mas-Coma S, Miles MA. Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae. Parasit Vectors 2021; 14:195. [PMID: 33832518 PMCID: PMC8034103 DOI: 10.1186/s13071-021-04647-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background Triatomine bugs, the vectors of Chagas disease, associate with vertebrate hosts in highly diverse ecotopes. It has been proposed that occupation of new microhabitats may trigger selection for distinct phenotypic variants in these blood-sucking bugs. Although understanding phenotypic variation is key to the study of adaptive evolution and central to phenotype-based taxonomy, the drivers of phenotypic change and diversity in triatomines remain poorly understood. Methods/results We combined a detailed phenotypic appraisal (including morphology and morphometrics) with mitochondrial cytb and nuclear ITS2 DNA sequence analyses to study Rhodnius ecuadoriensis populations from across the species’ range. We found three major, naked-eye phenotypic variants. Southern-Andean bugs primarily from vertebrate-nest microhabitats (Ecuador/Peru) are typical, light-colored, small bugs with short heads/wings. Northern-Andean bugs from wet-forest palms (Ecuador) are dark, large bugs with long heads/wings. Finally, northern-lowland bugs primarily from dry-forest palms (Ecuador) are light-colored and medium-sized. Wing and (size-free) head shapes are similar across Ecuadorian populations, regardless of habitat or phenotype, but distinct in Peruvian bugs. Bayesian phylogenetic and multispecies-coalescent DNA sequence analyses strongly suggest that Ecuadorian and Peruvian populations are two independently evolving lineages, with little within-lineage phylogeographic structuring or differentiation. Conclusions We report sharp naked-eye phenotypic divergence of genetically similar Ecuadorian R. ecuadoriensis (nest-dwelling southern-Andean vs palm-dwelling northern bugs; and palm-dwelling Andean vs lowland), and sharp naked-eye phenotypic similarity of typical, yet genetically distinct, southern-Andean bugs primarily from vertebrate-nest (but not palm) microhabitats. This remarkable phenotypic diversity within a single nominal species likely stems from microhabitat adaptations possibly involving predator-driven selection (yielding substrate-matching camouflage coloration) and a shift from palm-crown to vertebrate-nest microhabitats (yielding smaller bodies and shorter and stouter heads). These findings shed new light on the origins of phenotypic diversity in triatomines, warn against excess reliance on phenotype-based triatomine-bug taxonomy, and confirm the Triatominae as an informative model system for the study of phenotypic change under ecological pressure. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04647-z.
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Affiliation(s)
- Fernando Abad-Franch
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil. .,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fernando A Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil. .,Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA.
| | - Márcio G Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - James S Patterson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Dolores Bargues
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - M Ángeles Zuriaga
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Marcelo Aguilar
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador.,Instituto Juan César García, Quito, Ecuador
| | - Charles B Beard
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA
| | - Santiago Mas-Coma
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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190
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Kim A, Degnan JH. Heuristics for unrooted, unranked, and ranked anomaly zones under birth-death models. Mol Phylogenet Evol 2021; 161:107162. [PMID: 33831548 DOI: 10.1016/j.ympev.2021.107162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 10/21/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Species trees that can generate a nonmatching gene tree topology that is more probable than the topology matching the species tree are said to be in an anomaly zone. We introduce some heuristic approaches to infer whether species trees are in anomaly zones when it is difficult or impossible to compute the entire distribution of gene tree topologies. Here, probabilities of unrooted, unranked, and ranked gene tree topologies under the multispecies coalescent are used. A ranked tree can be viewed as an unranked tree with a temporal ordering of its internal nodes. Overall, considering probabilities of unrooted or unranked gene tree topologies within one nearest neighbor interchange from the species tree topology is a reasonable heuristic to infer the existence of anomalous unrooted or unranked gene trees, respectively. We investigated a test proposed by Linkem et al. (2016) which classifies a species tree as being in an unranked anomaly zone if there is a subset of four taxa in an unranked anomaly zone. We find this test to have high true positive rates, but it can also have high false positive rates. For ranked trees, because at least one of the most probable ranked gene tree topologies must have the same unranked topology as the species tree, we propose to use only those ranked gene trees that have topologies that match the unranked species tree topology. We find that the probability that the species tree is in unrooted and unranked anomaly zones tends to increase with the speciation rate, and the probability of all three types of anomaly zones increases rapidly with the number of taxa. We find that probabilities that species trees are in an anomaly zone can be quite high for moderately high speciation rates.
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Affiliation(s)
- Anastasiia Kim
- Department of Mathematics and Statistics, University of New Mexico, United States
| | - James H Degnan
- Department of Mathematics and Statistics, University of New Mexico, United States
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191
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Bannikova AA, Zemlemerova ED, Lebedev VS, Lavrenchenko LA. The phylogenetic relationships within the Eastern Afromontane clade of Crocidura based on mitochondrial and nuclear data. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00120-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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192
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Cicconardi F, Krapf P, D'Annessa I, Gamisch A, Wagner HC, Nguyen AD, Economo EP, Mikheyev AS, Guénard B, Grabherr R, Andesner P, Wolfgang A, Di Marino D, Steiner FM, Schlick-Steiner BC. Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations. Mol Biol Evol 2021; 37:2211-2227. [PMID: 32181804 PMCID: PMC7403626 DOI: 10.1093/molbev/msaa076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesized two parallel patterns would occur in a genome adapting to an extreme habitat: 1) strong positive selection on genes related to adaptation and 2) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetically related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared with all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has 1) a higher level of expression for stv and other heat-shock proteins in chill-shock tests and 2) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonization of high-altitude environments.
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Affiliation(s)
| | - Patrick Krapf
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Ilda D'Annessa
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", CNR (SCITEC-CNR), Milan, Italy
| | - Alexander Gamisch
- Department of Ecology, University of Innsbruck, Innsbruck, Austria.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Herbert C Wagner
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andrew D Nguyen
- Department of Entomology and Nematology, University of Florida, Gainesville, FL
| | - Evan P Economo
- Biodiversity & Biocomplexity Unit, Okinawa Institute of Science & Technology, Onna, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science & Technology, Onna, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Reingard Grabherr
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Philipp Andesner
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Daniele Di Marino
- Department of Life and Environmental Sciences - New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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193
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Takayama K, Tateishi Y, Kajita T. Global phylogeography of a pantropical mangrove genus Rhizophora. Sci Rep 2021; 11:7228. [PMID: 33785819 PMCID: PMC8009884 DOI: 10.1038/s41598-021-85844-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.
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Affiliation(s)
- Koji Takayama
- grid.258799.80000 0004 0372 2033Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yoichi Tateishi
- grid.267625.20000 0001 0685 5104Faculty of Education, University of the Ryukyus, Senbaru 1, Nakagami-gun, Okinawa, 903-0129 Japan
| | - Tadashi Kajita
- grid.267625.20000 0001 0685 5104Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, 870 Uehara, Taketomi-cho, Yaeyama-gun, Okinawa, 907-1541 Japan ,grid.258333.c0000 0001 1167 1801United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
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194
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Salvi D, Pinho C, Mendes J, Harris DJ. Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models. Mol Phylogenet Evol 2021; 161:107169. [PMID: 33798673 DOI: 10.1016/j.ympev.2021.107169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/17/2021] [Accepted: 03/25/2021] [Indexed: 11/15/2022]
Abstract
Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.
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Affiliation(s)
- Daniele Salvi
- University of L'Aquila, Department of Health, Life and Environmental Sciences, 67100 Coppito, L'Aquila, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Joana Mendes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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195
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Baroni S, Damasceno RP, Almeida-Toledo LFD. Paraphyly and evolutionary independent lineages in Gymnotus pantherinus (Gymnotiformes: Gymnotidae) in the Brazilian Atlantic Forest Coastal Streams. Mol Phylogenet Evol 2021; 161:107159. [PMID: 33794394 DOI: 10.1016/j.ympev.2021.107159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022]
Abstract
In the Brazilian Atlantic Forest (AF), many terrestrial species with broad geographical distributions show high diversity and endemism of intraspecific lineages, as revealed by molecular genetic data. This pattern, however, is less explored in freshwater fishes. Gymnotus pantherinus is an electric fish endemic to the Brazilian coastal drainages that shows a wide distribution, ranging from the states of Bahia to Santa Catarina, an unusual pattern for AF fishes. It has been hypothesized that G. pantherinus is a species complex because distinct morphotypes were described for the species based on morphometric and meristic features. We used mitochondrial and nuclear data to test this hypothesis. Based on phylogenetic inference and multi-locus, multispecies coalescent methods, we identified six independent lineages, flagging them as candidate species. One such lineage is the recently described species G. refugio that is nested within G. pantherinus and renders it paraphyletic, showing it is a species complex. We named G. pantherinus stricto sensu the lineage that includes samples from the type locality (Santos, SP). Our results show that genetic lineages correspond only partially and far exceed the number of previously reported morphotypes. Genetic breaks in the group correspond to landscape features associated with the Serra do Mar mountain range and with riverine dynamics caused by sea level changes during the last glacial maximum. Moreover, we found evidence of river capture events affecting phylogeographic structure in the group. We uncovered an important dimension of diversity in the group and encourage further integration of genetic and phenotypic data. Such integration is a fruitful approach not only to reduce the gap between taxonomy and evolutionary history in Gymnotidae, but also to uncover the real AF biodiversity.
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Affiliation(s)
- Sabrina Baroni
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.
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196
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Boulaassafer K, Ghamizi M, Machordom A, Albrecht C, Delicado D. Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00490-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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197
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Mitchell JK, Garrido-Benavent I, Quijada L, Pfister DH. Sareomycetes: more diverse than meets the eye. IMA Fungus 2021; 12:6. [PMID: 33726866 PMCID: PMC7961326 DOI: 10.1186/s43008-021-00056-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/16/2021] [Indexed: 01/16/2023] Open
Abstract
Since its resurrection, the resinicolous discomycete genus Sarea has been accepted as containing two species, one with black apothecia and pycnidia, and one with orange. We investigate this hypothesis using three ribosomal (nuITS, nuLSU, mtSSU) regions from and morphological examination of 70 specimens collected primarily in Europe and North America. The results of our analyses support separation of the traditional Sarea difformis s.lat. and Sarea resinae s.lat. into two distinct genera, Sarea and Zythia. Sarea as circumscribed is shown to conservatively comprise three phylospecies, with one corresponding to Sarea difformis s.str. and two, morphologically indistinguishable, corresponding to the newly combined Sarea coeloplata. Zythia is provisionally maintained as monotypic, containing only a genetically and morphologically variable Z. resinae. The new genus Atrozythia is erected for the new species A. klamathica. Arthrographis lignicola is placed in this genus on molecular grounds, expanding the concept of Sareomycetes by inclusion of a previously unknown type of asexual morph. Dating analyses using additional marker regions indicate the emergence of the Sareomycetes was roughly concurrent with the diversification of the genus Pinus, suggesting that this group of fungi emerged to exploit the newly-available resinous ecological niche supplied by Pinus or another, extinct group of conifers. Our phylogeographic studies also permitted us to study the introductions of these fungi to areas where they are not native, including Antarctica, Cape Verde, and New Zealand and are consistent with historical hypotheses of introduction.
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Affiliation(s)
- James K Mitchell
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA. .,Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA, 02138, USA.
| | - Isaac Garrido-Benavent
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE) & Dept. Botànica i Geologia, Universitat de València, C/ Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - Luis Quijada
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Donald H Pfister
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
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198
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Perea S, Sousa‐Santos C, Robalo J, Doadrio I. Historical biogeography of the Iberian Peninsula: multilocus phylogeny and ancestral area reconstruction for the freshwater fish genus
Squalius
(Actinopterygii, Leuciscidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvia Perea
- Museo Nacional de Ciencias Naturales, Biodiversity and Evolutionary Department 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
- Museo Nacional de Ciencias Naturales, Biodiversity and Evolutionary Department Madrid Spain
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199
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Koblmüller S, Schöggl CA, Lorber CJ, Van Steenberge M, Kmentová N, Vanhove MPM, Zangl L. African lates perches (Teleostei, Latidae, Lates): Paraphyly of Nile perch and recent colonization of Lake Tanganyika. Mol Phylogenet Evol 2021; 160:107141. [PMID: 33711447 DOI: 10.1016/j.ympev.2021.107141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022]
Abstract
Lates perches of the genus Lates (Latidae) are large piscivorous fishes, with a strikingly disjunct distribution range in coastal areas and estuaries of the Indo-Pacific region and in some large African freshwater systems. Previous phylogenetic hypotheses based on osteological and ontogenetic data suggested paraphyly of the African representatives, or even the small Lake Tanganyika species assemblage, with respect to the remaining Lates species. Based on a multilocus phylogeny, however, we show that extant African lates perches are monophyletic. The Nile perch, L. niloticus, which is widely distributed in the Nilo-Sudan region and Central Africa, comprises three distinct lineages and is paraphyletic with respect to the four endemic Lake Tanganyika species. We find that diversification of extant African Lates happened only as recently as the Pliocene. With the extensive, in part much older fossil record, this suggests repeated extinction and (re-)colonization of hydrological systems. We further find that Lates started to diversify in Lake Tanganyika only in the Pleistocene, which is much more recent than other fish radiations endemic to Lake Tanganyika, implying that they radiated in the presence of other top predators already in this ecosystem.
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Affiliation(s)
- Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | - Christian A Schöggl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Clemens J Lorber
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Maarten Van Steenberge
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium; Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, Helsinki FI-00014, Finland
| | - Lukas Zangl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria; Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045 Graz, Austria; ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria
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200
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Freitas FV, Branstetter MG, Griswold T, Almeida EAB. Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae). Mol Biol Evol 2021; 38:1090-1100. [PMID: 33179746 PMCID: PMC7947843 DOI: 10.1093/molbev/msaa277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
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Affiliation(s)
- Felipe V Freitas
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Terry Griswold
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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