201
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Fišer C, Robinson CT, Malard F. Cryptic species as a window into the paradigm shift of the species concept. Mol Ecol 2018; 27:613-635. [DOI: 10.1111/mec.14486] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Cene Fišer
- SubBio Lab; Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Christopher T. Robinson
- Department of Aquatic Ecology; Eawag; Dübendorf Switzerland
- Institute of Integrative Biology; ETH Zürich; Zürich Switzerland
| | - Florian Malard
- Université Lyon; Université Claude Bernard Lyon 1; CNRS; ENTPE; UMR5023 LEHNA Villeurbanne France
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202
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Hubka V, Nováková A, Jurjević Ž, Sklenář F, Frisvad JC, Houbraken J, Arendrup MC, Jørgensen KM, Siqueira JPZ, Gené J, Kolařík M. Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov. Int J Syst Evol Microbiol 2018; 68:995-1011. [PMID: 29458472 DOI: 10.1099/ijsem.0.002583] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves and clinical material. The A. candidus sensu lato isolates were characterized by DNA sequencing of four genetic loci, and agreement between molecular species delimitation results, morphological characters and exometabolite spectra were studied. Classical phylogenetic methods (maximum likelihood, Bayesian inference) and species delimitation methods based on the multispecies coalescent model supported recognition of up to three species in A. candidus sensu lato. After evaluation of phenotypic data, a broader species concept was adopted, and only one new species, Aspergillus dobrogensis, was proposed. This species is represented by 22 strains originating from seven countries (ex-type strain CCF 4651T=NRRL 62821T=IBT 32697T=CBS 143370T) and its differentiation from A. candidus is relevant for bioprospecting studies because these species have different exometabolite profiles. Evaluation of the antifungal susceptibility of section Candidi members to six antifungals using the reference EUCAST method showed that all species have low minimum inhibitory concentrations for all tested antifungals. These results suggest applicability of a wide spectrum of antifungal agents for treatment of infections caused by species from section Candidi.
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Affiliation(s)
- Vit Hubka
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alena Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - František Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Maiken 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
| | | | - João P Z Siqueira
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain.,Laboratório de Microbiologia, Faculdade de Medicina de SãoJosé do Rio Preto, São José do Rio Preto, Brazil
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Miroslav Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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203
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Magain N, Miadlikowska J, Goffinet B, Sérusiaux E, Lutzoni F. Macroevolution of Specificity in Cyanolichens of the Genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota). Syst Biol 2018; 66:74-99. [PMID: 28173598 DOI: 10.1093/sysbio/syw065] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/06/2015] [Accepted: 07/17/2016] [Indexed: 01/21/2023] Open
Abstract
Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts are more specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributions compared with generalist species.
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Affiliation(s)
- N Magain
- Evolution and Conservation Biology, University of Liège, Liège, Belgium.,Department of Biology, Duke University, Durham, NC, USA
| | - J Miadlikowska
- Evolution and Conservation Biology, University of Liège, Liège, Belgium
| | - B Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - E Sérusiaux
- Evolution and Conservation Biology, University of Liège, Liège, Belgium
| | - F Lutzoni
- Department of Biology, Duke University, Durham, NC, USA
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204
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Ballesteros JA, Hormiga G. Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae). Mol Phylogenet Evol 2018; 121:183-197. [PMID: 29337274 DOI: 10.1016/j.ympev.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States; Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, United States.
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States
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205
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Musher LJ, Cracraft J. Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus). Mol Phylogenet Evol 2018; 118:204-221. [DOI: 10.1016/j.ympev.2017.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022]
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206
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Sato S, Buckman-Young RS, Harvey MS, Giribet G. Cryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora : Peripatopsidae : Kumbadjena). INVERTEBR SYST 2018. [DOI: 10.1071/is18024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.
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207
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Inoue K, Hayes DM, Harris JL, Johnson NA, Morrison CL, Eackles MS, King TL, Jones JW, Hallerman EM, Christian AD, Randklev CR. The Pleurobemini (Bivalvia : Unionida) revisited: molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species. INVERTEBR SYST 2018. [DOI: 10.1071/is17059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.
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208
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Kajtoch Ł, Montagna M, Wanat M. Species delimitation within the Bothryorrhynchapion weevils: Multiple evidence from genetics, morphology and ecological associations. Mol Phylogenet Evol 2017; 120:354-363. [PMID: 29274498 DOI: 10.1016/j.ympev.2017.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/07/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022]
Abstract
Curculionidae is a hyperdiverse group of beetles, whose taxonomy and phylogenetics are still poorly understood, especially at the genus level. The latest work on the evolution of Apionini showed a noticeable "mess" in the subtribe Oxystomatina, where most of the morphology-based genera were found to be polyphyletic or paraphyletic. These discrepancies between classical taxonomy and molecular phylogenetics implied the need for further taxonomic revision of these groups. Here, we used sets of morphological, molecular and ecological characters to verify the taxonomic statuses and disentangle the phylogenetic relations among the Bothryorrhynchapion apionids, which are classified as a subgenus of Cyanapion. Morphological data including morphometrics, and multilocus molecular analyses confirmed the monophyly of the Bothryorrhynchapion and species statuses of five species. The morphological analyses showed that Cyanapion (Bothryorrhynchapion) protractum (Sharp, 1891) from the southeast Palaearctic is a synonym of C. (B.) gyllenhalii (Kirby). Moreover, ecological features (host plant use and presence/absence of the endosymbiotic bacteria Wolbachia) helped to unravel the relations among the examined weevils. The speciation of Bothryorrhynchapion apionids was probably affected by allopatric distribution, shifts in the preferred host plants (Vicia sp. or Lathyrus sp.) of sympatric taxa, and infection by different strains of Wolbachia. The paper presents the first comprehensive description of the species' morphology, biology and ecology, and includes a key to the species.
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Affiliation(s)
- Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland.
| | - Matteo Montagna
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, Via Celoria 2, 20133 Milan, Italy.
| | - Marek Wanat
- Museum of Natural History, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland.
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209
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Suárez-Villota EY, Carmignotto AP, Brandão MV, Percequillo AR, Silva MJDJ. Systematics of the genus Oecomys (Sigmodontinae: Oryzomyini): molecular phylogenetic, cytogenetic and morphological approaches reveal cryptic species. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elkin Y Suárez-Villota
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Edificio Emilio Pugín, campus Isla Teja, Valdivia, Chile
| | - Ana Paula Carmignotto
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Marcus Vinícius Brandão
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biolόgicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias, Piracicaba, São Paulo, Brazil
| | - Maria José de J Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
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210
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Species diversity in the marine microturbellarian Astrotorhynchus bifidus sensu lato (Platyhelminthes: Rhabdocoela) from the Northeast Pacific Ocean. Mol Phylogenet Evol 2017; 120:259-273. [PMID: 29248627 DOI: 10.1016/j.ympev.2017.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/26/2017] [Accepted: 12/10/2017] [Indexed: 12/21/2022]
Abstract
Increasing evidence suggests that many widespread species of meiofauna are in fact regional complexes of (pseudo-)cryptic species. This knowledge has challenged the 'Everything is Everywhere' hypothesis and also partly explains the meiofauna paradox of widespread nominal species with limited dispersal abilities. Here, we investigated species diversity within the marine microturbellarian Astrotorhynchus bifidus sensu lato in the Northeast Pacific Ocean. We used a multiple-evidence approach combining multi-gene (18S, 28S, COI) phylogenetic analyses, several single-gene and multi-gene species delimitation methods, haplotype networks and conventional taxonomy to designate Primary Species Hypotheses (PSHs). This included the development of rhabdocoel-specific COI barcode primers, which also have the potential to aid in species identification and delimitation in other rhabdocoels. Secondary Species Hypotheses (SSHs) corresponding to morphospecies and pseudo-cryptic species were then proposed based on the minimum consensus of different PSHs. Our results showed that (a) there are at least five species in the A. bifidus complex in the Northeast Pacific Ocean, four of which can be diagnosed based on stylet morphology, (b) the A. bifidus complex is a mixture of sympatric and allopatric species with regional and/or subglobal distributions, (c) sympatry occurs on local (sample sites), regional (Northeastern Pacific) and subglobal (Northern Atlantic, Arctic, Northeastern Pacific) scales. Mechanisms for this co-occurrence are still poorly understood, but we hypothesize they could include habitat differentiation (spatial and/or seasonal) and life history characteristics such as sexual selection and dispersal abilities. Our results also suggest the need for improved sampling and exploration of molecular markers to accurately map gene flow and broaden our understanding of species diversity and distribution of microturbellarians in particular and meiofauna in general.
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211
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SimÓ-Riudalbas M, Tarroso P, Papenfuss T, Al-Sariri T, Carranza S. Systematics, biogeography and evolution of Asaccus gallagheri (Squamata, Phyllodactylidae) with the description of a new endemic species from Oman. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1403496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marc SimÓ-Riudalbas
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Pedro Tarroso
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Vila do Conde, Portugal
| | - Theodore Papenfuss
- Department of Integrative Biology, Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Thuraya Al-Sariri
- Ministry of Environment and Climate Affairs, Thaqafah Street, 100, Muscat, Oman
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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212
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da Silva R, Peloso PLV, Sturaro MJ, Veneza I, Sampaio I, Schneider H, Gomes G. Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1108-1114. [PMID: 29216781 DOI: 10.1080/24701394.2017.1413364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern. Our results show incongruences among methods. ABGD, PTP and mPTP trend towards a lower number of estimated species. Phylogenetic-coalescent methods with single threshold were majority congruent for a same number of lineages. On the other hand, algorithms with multiple thresholds tend to estimate a higher number of potential species. We do not endorse the use of single-locus for species delimitation, but we do reinforce that single-locus data is sufficient to flag many problems.
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Affiliation(s)
- Raimundo da Silva
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
| | - Pedro L V Peloso
- b Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém , Brazil
| | | | - Ivana Veneza
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
| | - Iracilda Sampaio
- d Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará , Bragança , Brazil
| | - Horacio Schneider
- d Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará , Bragança , Brazil
| | - Grazielle Gomes
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
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213
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Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. Mol Phylogenet Evol 2017; 117:10-29. [DOI: 10.1016/j.ympev.2017.08.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
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214
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Sweet AD, Boyd BM, Allen JM, Villa SM, Valim MP, Rivera-Parra JL, Wilson RE, Johnson KP. Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution. Evolution 2017; 72:95-112. [PMID: 29094340 DOI: 10.1111/evo.13386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 02/05/2023]
Abstract
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.
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Affiliation(s)
- Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820
| | - Bret M Boyd
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Department of Entomology, University of Georgia, Athens, Georgia 30602
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Scott M Villa
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Michel P Valim
- Biotério da Universidade Iguaçu, Av. Abílio Augusto Távora, 2134, RJ 26275, Brazil
| | - Jose L Rivera-Parra
- Departamento de Petroleos, Facultad de Geologia y Petroleos, Escuela Politecnica Nacional, Quito, Ecuador
| | - Robert E Wilson
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820
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215
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Molecular phylogeny of Candidula (Geomitridae) land snails inferred from mitochondrial and nuclear markers reveals the polyphyly of the genus. Mol Phylogenet Evol 2017; 118:357-368. [PMID: 29107619 DOI: 10.1016/j.ympev.2017.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/08/2017] [Accepted: 10/23/2017] [Indexed: 11/21/2022]
Abstract
The genus Candidula (Geomitridae), consisting of 28 species in Western Europe as currently described, has a disjunct distribution in the Iberian Peninsula, Italy, the Balkans, the Aegean Islands, and one species on the Canary Islands. Although the genus is seemingly well defined by characters of the reproductive system, the relationships within the genus are still unclear and some authors have indicated a possible subgeneric division based on the internal morphology of the dart sac. Despite substantial phylogenetic incongruence, we present a well-resolved molecular phylogeny of Candidula based on two mitochondrial genes (COI and 16S rRNA), the nuclear rDNA region (5.8S rNRA + ITS2 + 28S rRNA) and seven additional nuclear DNA regions developed specifically for this genus (60SL13, 60SL17, 60SL7, RPL14, 40SS6, 60SL9, 60SL13a), in total 5595 bp. Six reciprocally monophyletic entities including Candidula species were recovered, grouping into two major clades. The incorporation of additional geomitrid genera allowed us to unequivocally demonstrate the polyphyly of the genus Candidula. One major clade grouped species from southern France and Italy with the widely distributed species C. unifasciata. The second major clade grouped all the species from the Iberian Peninsula, including C. intersecta and C. gigaxii. Candidula ultima from the Canary Islands was recovered as separated lineage within the latter clade and related to African taxa. The six monophyla were defined as six new genera belonging to different tribes within the Helicellinae. Thus, we could show that similar structures of the stimulatory apparatus of the genital system in different taxa do not necessarily indicate a close phylogenetic relationship in the Geomitridae. More genera of the family are needed to clarify their evolutionary relationships, and to fully understand the evolution of the stimulatory apparatus of the genital system within the Geomitridae.
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216
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Guzmán NV, Pietrokovsky SM, Cigliano MM, Confalonieri VA. Unraveling the diversification history of grasshoppers belonging to the " Trimerotropis pallidipennis" (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes. PeerJ 2017; 5:e3835. [PMID: 28975055 PMCID: PMC5624295 DOI: 10.7717/peerj.3835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022] Open
Abstract
The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
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Affiliation(s)
- Noelia Verónica Guzmán
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
| | - Silvia Mónica Pietrokovsky
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
| | - Maria Marta Cigliano
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Museo de La Plata, Universidad Nacional de la Plata, Centro de Estudios Parasitológicos y de Vectores (CEPAVE), La Plata, Buenos Aires, Argentina
| | - Viviana Andrea Confalonieri
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Ecología, Genética y Evolución (IEGEBA), Buenos Aires, Argentina
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217
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Abstract
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
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Key Words
- Aspergillus canadensis Visagie, Yilmaz, F. Sklenar & Seifert
- Aspergillus clavatophorus F. Sklenar, S.W. Peterson & Hubka
- Aspergillus destruens Zalar, F. Sklenar, S.W. Peterson & Hubka
- Aspergillus domesticus F. Sklenar, Houbraken, Zalar & Hubka
- Aspergillus glabripes F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus hordei F. Sklenar, S.W. Peterson & Hubka
- Aspergillus infrequens F. Sklenar, S.W. Peterson & Hubka
- Aspergillus magnivesiculatus F. Sklenar, Zalar, Ž. Jurjević & Hubka
- Aspergillus pachycaulis F. Sklenar, S.W. Peterson, Ž. Jurjević & Hubka
- Aspergillus penicillioides
- Aspergillus pseudogracilis F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus restrictus
- Aspergillus reticulatus F. Sklenar, Ž. Jurjević, S.W. Peterson & Hubka
- Aspergillus salinicola Zalar, F. Sklenar, Visagie & Hubka
- Aspergillus tardicrescens F. Sklenar, Houbraken, Zalar, & Hubka
- Aspergillus villosus F. Sklenar, S.W. Peterson & Hubka
- Eurotium
- food spoilage
- indoor fungi
- linear discriminant analysis
- multigene phylogeny
- multispecies coalescent model
- sick building syndrome
- xerophilic fungi
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218
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Conte-Grand C, Britz R, Dahanukar N, Raghavan R, Pethiyagoda R, Tan HH, Hadiaty RK, Yaakob NS, Rüber L. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions. PLoS One 2017; 12:e0184017. [PMID: 28931084 PMCID: PMC5606936 DOI: 10.1371/journal.pone.0184017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/16/2017] [Indexed: 11/19/2022] Open
Abstract
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
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Affiliation(s)
| | - Ralf Britz
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, India.,Systematics, Ecology & Conservation Laboratory, Zoo Outreach Organization, Saravanampatti, Coimbatore, Tamil Nadu, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Renny K Hadiaty
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Norsham S Yaakob
- Forest Research Institute Malaysia, Kepong, Kuala Lumpur, Malaysia
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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219
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The effects of Quaternary sea-level fluctuations on the evolutionary history of an endemic ground lizard (Tropidurus hygomi). ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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220
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Gehara M, Garda AA, Werneck FP, Oliveira EF, Fonseca EM, Camurugi F, Magalhães FDM, Lanna FM, Sites JW, Marques R, Silveira‐Filho R, São Pedro VA, Colli GR, Costa GC, Burbrink FT. Estimating synchronous demographic changes across populations using
hABC
and its application for a herpetological community from northeastern Brazil. Mol Ecol 2017; 26:4756-4771. [DOI: 10.1111/mec.14239] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/30/2017] [Accepted: 07/02/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Marcelo Gehara
- Department of Herpetology American Museum of Natural History New York NY USA
| | - Adrian A. Garda
- Departamento de Botânica e Zoologia Centro de Biociências Universidade Federal do Rio Grande do Norte Lagoa Nova Natal RN Brazil
| | - Fernanda P. Werneck
- Coordenação de Biodiversidade Programa de Coleções Científicas Biológicas Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus AM Brazil
| | - Eliana F. Oliveira
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências Biológicas e da Saúde Laboratório de Zoologia Cidade Universitária Universidade Federal do Mato Grosso do Sul Campo Grand MS Brazil
| | - Emanuel M. Fonseca
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Felipe Camurugi
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Felipe de M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Flávia M. Lanna
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum Brigham Young University Provo UT USA
| | - Ricardo Marques
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Ricardo Silveira‐Filho
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Vinícius A. São Pedro
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências da Natureza Universidade Federal de São Carlos Buri SP Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Gabriel C. Costa
- Department of Biology Auburn University at Montgomery Montgomery AL USA
| | - Frank T. Burbrink
- Department of Herpetology American Museum of Natural History New York NY USA
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221
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Araujo R, Buckley D, Nagel KO, García-Jiménez R, Machordom A. Species boundaries, geographic distribution and evolutionary history of the Western Palaearctic freshwater mussels Unio (Bivalvia: Unionidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx039] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Rafael Araujo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - David Buckley
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | | | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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222
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Bernardes SC, Pepato AR, von Rintelen T, von Rintelen K, Page TJ, Freitag H, de Bruyn M. The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species. Sci Rep 2017; 7:9044. [PMID: 28831142 PMCID: PMC5567278 DOI: 10.1038/s41598-017-08494-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/30/2017] [Indexed: 11/09/2022] Open
Abstract
The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.
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Affiliation(s)
- Samuel C Bernardes
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil.
| | - Almir R Pepato
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Kristina von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia.,Water Planning Ecology, Queensland Department of Science, Information Technology and Innovation, Dutton Park, Queensland 4102, Australia
| | - Hendrik Freitag
- Department of Biology, School of Science & Engineering, Ateneo de Manila University, Quezon City, 1108, Philippines
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK. .,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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223
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Eyer PA, Seltzer R, Reiner-Brodetzki T, Hefetz A. An integrative approach to untangling species delimitation in the Cataglyphis bicolor desert ant complex in Israel. Mol Phylogenet Evol 2017; 115:128-139. [PMID: 28774791 DOI: 10.1016/j.ympev.2017.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/22/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Although extensive research has been carried out on the desert ants in the genus Cataglyphis in recent years, some of the specific intra- and interspecific relationships remain elusive. The present study disentangles the phylogenetic relationships among the C. bicolor complex in Israel using an integrative approach based on genetic markers, morphometric measurements, and chemical analyses (cuticular hydrocarbons). Several species delimitation approaches based on four nuclear, two mitochondrial, and eleven microsatellite markers, as well as 16 body measurements and 56 chemical variables, were employed to deciphering the occurrence of cryptic species in our data set. Our findings support the occurrence of at least four distinct species in the C. bicolor group in Israel, one of which may be a complex of three more recent species. The findings confirm the distinctiveness of C. isis and C. holgerseni. They attest the presence of a recently discovered species, C. israelensis, in the central mountain ridge and the occurrence of another clade distributed from the Negev to the Mediterranean coast, comprising the species C. niger, C. savignyi, and C. drusus. Although these three species are separated on the basis of mtDNA, this subgrouping was not supported by any of the nuclear sequence markers nor by the microsatellite analysis. This genetic structure may thus either reflect a possible recent speciation, or a geographical structuring of a single species. Overall, using these different sources of evidence we locate our samples within a global phylogeny of the bicolor group and discuss the processes that underlie speciation in this group.
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Affiliation(s)
- P A Eyer
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - R Seltzer
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - T Reiner-Brodetzki
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - A Hefetz
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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224
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Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil. Mol Phylogenet Evol 2017; 112:68-78. [DOI: 10.1016/j.ympev.2017.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 11/18/2022]
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225
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Hsu TH, Gwo JC. Genetic diversity and stock identification of small abalone (Haliotis diversicolor) in Taiwan and Japan. PLoS One 2017; 12:e0179818. [PMID: 28662122 PMCID: PMC5491045 DOI: 10.1371/journal.pone.0179818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 06/05/2017] [Indexed: 11/19/2022] Open
Abstract
Small abalone (Haliotis diversicolor) is a commercially valuable species for both fisheries and aquaculture. The production of annual farmed small abalone in Taiwan, once the highest in the world, has dramatically decreased in the past 15 years, and currently, the industry is close to collapse. Understanding the genetic diversity of small abalone and developing stock identification methods will be useful for genetic breeding, restoring collapsed stocks, managing stocks, and preventing illegal trade. We investigated 307 cultured and wild individuals from Taiwan, Japan, and Bali Island (Indonesia) by using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis of mtDNA COI gene sequences revealed that the individuals collected from Taiwan, Japan, and Indonesia could be identified, and showed significant genetic divergence. In addition, the Indonesian population (Haliotis diversicolor squamata) was significantly different from the other populations and might need to be considered a separate species. We discovered a single nucleotide polymorphism marker in the mtDNA COI gene that can be used to distinguish the Taiwan population from the Japan population. We also developed a polymerase chain reaction-restriction fragment length polymorphism method for rapid detection. Furthermore, we could identify the cultured stocks, wild population, and hybrid stocks by using 6 microsatellites and amplified fragment length polymorphism. This study contributes useful tools for stock identification and the production of high-disease resistant small abalone strains (Japan × Taiwan or Taiwan × Japan). Efforts should be made to avoid unintentional random genetic mixing of the Taiwan population with the Japan population and subsequent breakdown of population differentiation, which impair local adaptation of the Taiwan wild population. Molecular markers revealed a split between the Taiwan and Japan populations, and the existence of a possible barrier to the free dispersal of small abalone is discussed.
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Affiliation(s)
- Te-Hua Hsu
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Jin-Chywan Gwo
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- * E-mail:
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226
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Irestedt M, Batalha-Filho H, Ericson PGP, Christidis L, Schodde R. Phylogeny, biogeography and taxonomic consequences in a bird-of-paradise species complex, Lophorina–Ptiloris (Aves: Paradisaeidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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227
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Malaney JL, Demboski JR, Cook JA. Integrative species delimitation of the widespread North American jumping mice (Zapodinae). Mol Phylogenet Evol 2017; 114:137-152. [PMID: 28600183 DOI: 10.1016/j.ympev.2017.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023]
Abstract
Delimiting species can be challenging, but is a key step for the critical examination of evolutionary history and for prioritizing conservation efforts. Because systematic relationships are often determined iteratively using tests based on taxonomy, such methods can fail to detect cryptic variation and result in biased conclusions. Conversely, discovery-based approaches provide a powerful way to define operational taxonomic units and test species boundaries. We compare both approaches (taxonomy-based delimitation - TBD and discovery-based delimitation - DBD) within North American jumping mice (Zapodinae) using broad sampling, multilocus analyses, and ecological tests. This group diversified through the dynamic glacial-interglacial periods of the Quaternary and phylogeographic tests reveal 28 lineages that correspond poorly with current taxonomy (4 species, 32 nominal subspecies). However, neither the 4-species or 28-lineage hypotheses are optimal for species-level classification. Rather, information theoretic approaches (Bayes Factors) indicate a 15-species hypothesis is best for characterizing genetic variation in this group, with subsequent iterative pairwise ecological tests failing to confirm four species pairs. Taken together, evolutionary and ecological tests capture divergence among 11 putative species that, if upheld by additional tests, will lead to taxonomic revision and reevaluation of conservation plans.
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Affiliation(s)
- Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA; Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA.
| | - Joseph A Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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228
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Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT. Positive association between population genetic differentiation and speciation rates in New World birds. Proc Natl Acad Sci U S A 2017; 114:6328-6333. [PMID: 28559330 PMCID: PMC5474768 DOI: 10.1073/pnas.1617397114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.
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Affiliation(s)
- Michael G Harvey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803;
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Glenn F Seeholzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
| | - Brian Tilston Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ornithology, American Museum of Natural History, New York, NY 10024
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Andrés M Cuervo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118
| | - Robb T Brumfield
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
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229
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Vieira C, Camacho O, Sun Z, Fredericq S, Leliaert F, Payri C, De Clerck O. Historical biogeography of the highly diverse brown seaweed Lobophora (Dictyotales, Phaeophyceae). Mol Phylogenet Evol 2017; 110:81-92. [PMID: 28279809 DOI: 10.1016/j.ympev.2017.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/22/2017] [Accepted: 03/04/2017] [Indexed: 11/23/2022]
Abstract
The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98-121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (-75 to -60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.
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Affiliation(s)
- Christophe Vieira
- ENTROPIE (IRD, UR, CNRS), LabEx-CORAIL, Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium; Sorbonne Universités, UPMC Univ Paris 06, IFD, Paris F75252, France.
| | - Olga Camacho
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-3602, USA
| | - Zhongmin Sun
- Institute of Oceanology, Chinese Academy of Sciences, Department of Marine Organism Taxonomy and Phylogeny, China
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-3602, USA
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium; Botanic Garden Meise, 1860 Meise, Belgium
| | - Claude Payri
- ENTROPIE (IRD, UR, CNRS), LabEx-CORAIL, Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium
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230
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Spatial conservation prioritization of biodiversity spanning the evolutionary continuum. Nat Ecol Evol 2017; 1:151. [PMID: 28812637 DOI: 10.1038/s41559-017-0151] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022]
Abstract
Accounting for evolutionary relationships between and within species is important for biodiversity conservation planning, but is rarely considered in practice. Here we introduce a novel framework to identify priority conservation areas accounting for phylogenetic and intraspecific diversity, integrating concepts from phylogeny, phylogeography, spatial statistics and spatial conservation prioritization. The framework allows planners to incorporate and combine different levels of evolutionary diversity and can be applied to any taxonomic group and to any region in the world. We illustrate our approach using amphibian and reptile species occurring in a biodiversity hotspot region, the Iberian Peninsula. We found that explicitly incorporating phylogenetic and intraspecific diversity in systematic conservation planning provides advantages in terms of maximizing overall biodiversity representation while enhancing its persistence and evolutionary potential. Our results emphasize the need to account for the evolutionary continuum in order to efficiently implement biodiversity conservation planning decisions.
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231
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Miranda EA, Ferreira KM, Carvalho AT, Martins CF, Fernandes CR, Del Lama MA. Pleistocene climate changes shaped the population structure of Partamona seridoensis (Apidae, Meliponini), an endemic stingless bee from the Neotropical dry forest. PLoS One 2017; 12:e0175725. [PMID: 28410408 PMCID: PMC5391937 DOI: 10.1371/journal.pone.0175725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/30/2017] [Indexed: 11/28/2022] Open
Abstract
Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup. The Mantel test revealed no isolation by distance. No evidence of a potential geographic barrier in the present that could explain the diversification between the P. seridoensis haplogroups was found. However, Pleistocene climatic changes may explain this differentiation, since the initial time for the P. seridoensis lineages diversification took place during the mid-Pleistocene, specifically the interglacial period, when the biota is presumed to have been more associated with dry conditions and had more restricted, fragmented geographical distribution. This event may have driven diversification by isolating the two haplogroups. Otherwise, the climatic changes in the late Pleistocene must not have drastically affected the population dynamics of P. seridoensis, since the Bayesian Skyline Plot did not reveal any substantial fluctuation in effective population size in either haplogroup. Considering its importance and the fact that it is an endemic bee from a very threatened Neotropical dry forest, the results herein could be useful to the development of conservation strategies for P. seridoensis.
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Affiliation(s)
- Elder Assis Miranda
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Kátia Maria Ferreira
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Airton Torres Carvalho
- Unidade Acadêmica de Serra Talhada, Universidade Federal Rural de Pernambuco, Serra Talhada, PE, Brazil
| | - Celso Feitosa Martins
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | | | - Marco Antonio Del Lama
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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232
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Sato H, Tanabe AS, Toju H. Host shifts enhance diversification of ectomycorrhizal fungi: diversification rate analysis of the ectomycorrhizal fungal genera Strobilomyces and Afroboletus with an 80-gene phylogeny. THE NEW PHYTOLOGIST 2017; 214:443-454. [PMID: 27918625 DOI: 10.1111/nph.14368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
Mutualisms with new host lineages can provide symbionts with novel ecological opportunities to expand their geographical distribution, thereby leading to evolutionary diversification. Because ectomycorrhizal (ECM) fungi provide ideal opportunities to test the relationship between host shifts and diversification, we tested whether mutualism with new host lineages could increase the diversification rates of ECM fungi. Using a Bayesian tree inferred from 23 027-base nucleotide sequences of 80 single-copy genes, we tested whether the diversification rate had changed through host-shift events in the monophyletic clade containing the ECM fungal genera Strobilomyces and Afroboletus. The results indicated that these fungi were initially associated with Caesalpinioideae/Monotoideae in Africa, acquired associations with Dipterocarpoideae in tropical Asia, and then switched to Fagaceae/Pinaceae and Nothofagaceae/Eucalyptus. Fungal lineages associated with Fagaceae/Pinaceae were inferred to have approximately four-fold and two-fold greater diversification rates than those associated with Caesalpinioideae/Monotoideae and Dipterocarpoideae or Nothofagaceae/Eucalyptus, respectively. Moreover, the diversification rate shift was inferred to follow the host shift to Fagaceae/Pinaceae. Our study suggests that host-shift events, particularly those occurring with respect to Fagaceae/Pinaceae, can provide ecological opportunities for the rapid diversification of Strobilomyces-Afroboletus. Although further studies are needed for generalization, we propose a possible diversification scenario of ECM fungi.
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Affiliation(s)
- Hirotoshi Sato
- Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan
- Department of Environmental Solution Technology, Facility of Science & Technology, Ryukoku University, Seta-Oe, Otsu, 520-2194, Shiga, Japan
| | - Akifumi S Tanabe
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4, Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Hirokazu Toju
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyoku Kyoto, 606-8501, Japan
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233
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Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT. A latitudinal phylogeographic diversity gradient in birds. PLoS Biol 2017; 15:e2001073. [PMID: 28406905 PMCID: PMC5390966 DOI: 10.1371/journal.pbio.2001073] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/10/2017] [Indexed: 01/06/2023] Open
Abstract
High tropical species diversity is often attributed to evolutionary dynamics over long timescales. It is possible, however, that latitudinal variation in diversification begins when divergence occurs within species. Phylogeographic data capture this initial stage of diversification in which populations become geographically isolated and begin to differentiate genetically. There is limited understanding of the broader implications of intraspecific diversification because comparative analyses have focused on species inhabiting and evolving in restricted regions and environments. Here, we scale comparative phylogeography up to the hemisphere level and examine whether the processes driving latitudinal differences in species diversity are also evident within species. We collected genetic data for 210 New World bird species distributed across a broad latitudinal gradient and estimated a suite of metrics characterizing phylogeographic history. We found that lower latitude species had, on average, greater phylogeographic diversity than higher latitude species and that intraspecific diversity showed evidence of greater persistence in the tropics. Factors associated with species ecologies, life histories, and habitats explained little of the variation in phylogeographic structure across the latitudinal gradient. Our results suggest that the latitudinal gradient in species richness originates, at least partly, from population-level processes within species and are consistent with hypotheses implicating age and environmental stability in the formation of diversity gradients. Comparative phylogeographic analyses scaled up to large geographic regions and hundreds of species can show connections between population-level processes and broad-scale species-richness patterns.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York, United States of America
| | - Glenn F. Seeholzer
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Michael G. Harvey
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrés M. Cuervo
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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234
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Biogeography and diversification dynamics of the African woodpeckers. Mol Phylogenet Evol 2017; 108:88-100. [DOI: 10.1016/j.ympev.2017.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/21/2016] [Accepted: 01/07/2017] [Indexed: 12/27/2022]
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235
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Blair C, Bryson RW. Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae:Phrynosoma). Mol Ecol Resour 2017; 17:1168-1182. [DOI: 10.1111/1755-0998.12658] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Blair
- Department of Biological Sciences; New York City College of Technology; The City University of New York; 300 Jay Street Brooklyn NY 11201 USA
- Biology PhD Program; CUNY Graduate Center; 365 5th Avenue New York NY 10016 USA
| | - Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; 4331 Memorial Way Northeast Seattle WA 98195 USA
- Moore Laboratory of Zoology; Occidental College; Los Angeles CA 90041 USA
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236
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Gélin P, Postaire B, Fauvelot C, Magalon H. Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Mol Phylogenet Evol 2017; 109:430-446. [PMID: 28219759 DOI: 10.1016/j.ympev.2017.01.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 01/06/2023]
Abstract
Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis.
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Affiliation(s)
- P Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - B Postaire
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - C Fauvelot
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Nouméa cedex, New Caledonia
| | - H Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France.
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237
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Manawatthana S, Laosinchai P, Onparn N, Brockelman WY, Round PD. Phylogeography of bulbuls in the genus Iole (Aves: Pycnonotidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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238
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Tarvin RD, Powell EA, Santos JC, Ron SR, Cannatella DC. The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs. Mol Phylogenet Evol 2017; 109:283-295. [PMID: 28089841 DOI: 10.1016/j.ympev.2016.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/30/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023]
Abstract
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.
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Affiliation(s)
- Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States.
| | - Emily A Powell
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States; Department of Biology, University of Miami, Miami, FL, United States
| | - Juan C Santos
- Department of Biology, Brigham Young University, Provo, UT, United States; Department of Biological Sciences, St. John's University, Queens, NY, United States
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States
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239
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Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0317-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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240
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Daniels SR, Dreyer M, Sharma PP. Contrasting the population genetic structure of two velvet worm taxa (Onychophora : Peripatopsidae : Peripatopsis) in forest fragments along the south-eastern Cape, South Africa. INVERTEBR SYST 2017. [DOI: 10.1071/is16085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
During the present study, we examined the phylogeography and systematics of two species of velvet worm (Peripatopsis Pocock, 1894) in the forested region of the southern Cape of South Africa. A total of 89 P. moseleyi (Wood-Mason, 1879) and 65 P. sedgwicki (Purcell, 1899) specimens were collected and sequenced for the cytochrome c oxidase subunit I mtDNA (COI). In addition, a single P. sedgwicki specimen per sample locality was sequenced for the 18S rRNA locus. Furthermore, morphological variation among P. sedgwicki sample localities were explored using traditional alpha taxonomic characters. DNA sequence data were subjected to phylogenetic analyses using Bayesian inference and population genetic analyses using haplotype networks and analyses of molecular variance (AMOVAs). Phylogenetic results revealed the presence of four and three clades within P. moseleyi and P. sedgwicki respectively. Haplotype networks were characterised by the absence of shared haplotypes between clades, suggesting genetic isolation, a result corroborated by the AMOVA and highly significant FST values. Specimens from Fort Fordyce Nature Reserve were both genetically and morphologically distinct from the two remaining P. sedgwicki clades. The latter result suggests the presence of a novel lineage nested within P. sedgwicki and suggests that species boundaries within this taxon require re-examination.
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241
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A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae). Mol Phylogenet Evol 2017; 106:28-43. [DOI: 10.1016/j.ympev.2016.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/18/2022]
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242
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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243
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Cornils A, Wend-Heckmann B, Held C. Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages? Mol Phylogenet Evol 2016; 107:473-485. [PMID: 28007567 DOI: 10.1016/j.ympev.2016.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 11/19/2022]
Abstract
Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.
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Affiliation(s)
- Astrid Cornils
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Britta Wend-Heckmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Christoph Held
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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244
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Renner MAM, Heslewood MM, Patzak SDF, Schäfer-Verwimp A, Heinrichs J. By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida). Mol Phylogenet Evol 2016; 107:576-593. [PMID: 28007566 DOI: 10.1016/j.ympev.2016.12.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/24/2022]
Abstract
As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila. GMYC from trees calculated using three different molecular clocks were compared, in some lineages different primary species hypotheses were returned by analyses of trees estimated under different clock models, suggesting clock model selection should be a routine component of phylogeny reconstruction for tree-based species delimitation methods, such as GMYC. Our results suggest that a minimum of 71 Plagiochilaceae species occur in Australasia, 16 more than currently accepted for the region, comprising 8 undetermined species and 8 synonyms requiring reinstatement. Despite modern taxonomic investigation over a four decade period, (1) real diversity is 29% higher than currently recognized; and (2) 12 of 33, or 36%, of currently accepted and previously untested Australasian species have circumscription issues, including polyphyly, paraphyly, internal phylogenetic structure, or combinations of two or more of these issues. These both reflect the many challenges associated with grouping decisions based solely on morphological data in morphologically simple yet polymorphic plant lineages. Our results highlight again the critical need for combined molecular-morphological datasets as a basis for resolving robust species hypotheses in species-rich bryophyte lineages.
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Affiliation(s)
- Matt A M Renner
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, NSW 2000, Australia.
| | - Margaret M Heslewood
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, NSW 2000, Australia
| | - Simon D F Patzak
- Ludwig Maximilian University, Faculty of Biology, Department of Biology and Geobio-Center, Menzinger Straβe 67, D-80638 Munich, Germany
| | | | - Jochen Heinrichs
- Ludwig Maximilian University, Faculty of Biology, Department of Biology and Geobio-Center, Menzinger Straβe 67, D-80638 Munich, Germany
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245
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Postaire B, Magalon H, Bourmaud CAF, Bruggemann JH. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa). Mol Phylogenet Evol 2016; 105:36-49. [DOI: 10.1016/j.ympev.2016.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/16/2016] [Accepted: 08/21/2016] [Indexed: 01/04/2023]
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246
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Gaubert P, Njiokou F, Ngua G, Afiademanyo K, Dufour S, Malekani J, Bi SG, Tougard C, Olayemi A, Danquah E, Djagoun CAMS, Kaleme P, Mololo CN, Stanley W, Luo SJ, Antunes A. Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification. Mol Ecol 2016; 25:5975-5993. [PMID: 27862533 DOI: 10.1111/mec.13886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 01/03/2023]
Abstract
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, BP 812, Yaoundé, Cameroon
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE), Barrio Ukomba, S/N, Bata, Equatorial Guinea
| | - Komlan Afiademanyo
- Département de Zoologie et de Biologie Animale, Université de Lomé, BP 1515, Lomé, Togo
| | | | - Jean Malekani
- Department of Biology, University of Kinshasa, PO Box 218, Kinshasa XI, Democratic Republic of Congo
| | - Sery Gonedelé Bi
- Laboratoire de Génétique, Université Félix Houphouët Boigny d'Abidjan-Cocody, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005, Ile-Ife, Nigeria
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 LEA-FSA, Cotonou, Benin
| | - Prince Kaleme
- Laboratoire de Mammalogie, Département de Biologie, Centre de Recherches en Sciences Naturelles (CRSN) - Lwiro, DS (Dépêche Spéciale) Bukavu, Democratic Republic of Congo.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Casimir Nebesse Mololo
- Université de Kisangani, Faculté des Sciences, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - William Stanley
- Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
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247
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Population genetics and geometric morphometrics of the Bombus ephippiatus species complex with implications for its use as a commercial pollinator. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0903-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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248
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Cryptic species diversity in sub-Antarctic islands: A case study of Lepidonotothen. Mol Phylogenet Evol 2016; 104:32-43. [DOI: 10.1016/j.ympev.2016.07.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/20/2016] [Accepted: 07/11/2016] [Indexed: 12/28/2022]
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249
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Prates I, Rivera D, Rodrigues MT, Carnaval AC. A mid‐
P
leistocene rainforest corridor enabled synchronous invasions of the
A
tlantic
F
orest by
A
mazonian anole lizards. Mol Ecol 2016; 25:5174-5186. [DOI: 10.1111/mec.13821] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Ivan Prates
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
| | - Danielle Rivera
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology University of Texas at Arlington 501 S. Nedderman Drive Arlington TX 76019 USA
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo Rua do Matão Travessa 14, n. 321 São Paulo SP 05508‐090 Brazil
| | - Ana C. Carnaval
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
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250
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Eyer PA, Leniaud L, Tinaut A, Aron S. Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants. Mol Phylogenet Evol 2016; 105:251-262. [PMID: 27591172 DOI: 10.1016/j.ympev.2016.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022]
Abstract
Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.
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Affiliation(s)
- P A Eyer
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium.
| | - L Leniaud
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
| | - A Tinaut
- Department of Animal Biology, Faculty of Sciences, University of Granada, E-18071 Granada, Spain
| | - S Aron
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
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