1
|
Marske KA, Boyer SL. Phylogeography reveals the complex impact of the Last Glacial Maximum on New Zealand’s terrestrial biota. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2079682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Sarah L. Boyer
- Biology Department, Macalester College, St. Paul, MN, USA
| |
Collapse
|
2
|
Seidel M, Sýkora V, Leschen RAB, Clarkson B, Fikáček M. Ancient relicts or recent immigrants? Different dating strategies alter diversification scenarios of New Zealand aquatic beetles (Coleoptera: Hydrophilidae: Berosus). Mol Phylogenet Evol 2021; 163:107241. [PMID: 34224848 DOI: 10.1016/j.ympev.2021.107241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/20/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022]
Abstract
Dated species-level phylogenies are crucial for understanding the origin and evolutionary history of modern faunas, yet difficult to obtain due to the frequent absence of suitable age calibrations at species level. Substitution rates of related or more inclusive clades are often used to overcome this limitation but the accuracy of this approach remains untested. We compared tree dating based on substitution rates with analyses implementing fossil data by direct node-dating and indirect root-age constraints for the New Zealand endemic Berosus water beetles (Coleoptera: Hydrophilidae). The analysis based solely on substitution rates indicated a Miocene colonization of New Zealand and Pleistocene origin of species. By contrast, all analyses that implemented fossil data resulted in significantly older age estimates, indicating an ancient early Cenozoic origin of the New Zealand clade, diversification of species during or after the Oligocene transgression and Miocene-Pliocene origin of within-species population structure. Rate-calibrated time trees were incongruent with recently published Coleoptera time trees, the fossil record of Berosus and the distribution of outgroup species. Strong variation of substitution rates among Coleoptera lineages, as well as among lineages within the family Hydrophilidae, was identified as the principal reason for low accuracy of rate-calibrated analyses, resulting in underestimated node ages in Berosus. We provide evidence that Oligocene to Pliocene events, rather than the Pleistocene Glacial cycles, played an essential role in the formation of the modern New Zealand insect fauna.
Collapse
Affiliation(s)
- Matthias Seidel
- Centrum für Naturkunde, Leibniz-Institut zur Analyse des Biodiversitätswandels, Martin-Luther-King Platz 3, Hamburg, Germany
| | - Vít Sýkora
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Richard A B Leschen
- Manaaki Whenua - Landcare Research, New Zealand Arthropod Collection, Auckland, New Zealand
| | - Bruno Clarkson
- Laboratório de Biodiversidade Entomológica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Martin Fikáček
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic; Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan; Department of Entomology, National Museum, Cirkusová 1740, Prague 9, Czech Republic.
| |
Collapse
|
3
|
Marske KA, Thomaz AT, Knowles LL. Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand. Mol Ecol 2020; 29:4665-4679. [PMID: 32991032 DOI: 10.1111/mec.15655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 08/23/2020] [Accepted: 09/07/2020] [Indexed: 01/23/2023]
Abstract
Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.
Collapse
Affiliation(s)
- Katharine A Marske
- Geographical Ecology Group, Department of Biology, University of Oklahoma, Norman, OK, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Andréa T Thomaz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá DC, Colombia
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
4
|
Chou MH, Yeh WB. Delineation of two new, highly similar species of Taiwanese Cylindera tiger beetles (Coleoptera, Carabidae, Cicindelinae) based on morphological and molecular evidence. Zookeys 2019; 875:31-62. [PMID: 31572044 PMCID: PMC6751220 DOI: 10.3897/zookeys.875.37856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/11/2019] [Indexed: 11/12/2022] Open
Abstract
Tiger beetles have been recognized primarily based on morphological characters. However, the variations of elytral maculation and coloration sometimes lead to misjudgment in species classification and the overlooking of the existence of cryptic species. Recently, specimens of two endemic species of Taiwanese Cylindera, C.sauteri and C.pseudocylindriformis, exhibit morphologically recognizable forms, indicating that some undescribed species may exist. To clarify their taxonomic status, morphological characteristics including male genitalia were examined and two mitochondrial genes, COI and 16S rDNA, and one nuclear 28S rDNA were analyzed. Molecular phylogenetic inferences indicated that both forms in both species are reciprocally monophyletic. Moreover, molecular dating showed the forms diverged approximately 1.3 million years ago. Two new species, Cylinderaooasp. nov. and Cylinderaautumnalissp. nov., are thereby described. The main recognizable characteristics separating C.ooasp. nov. from C.sauteri are the lack of a triangular spot at the middle edge of elytron and the elongated but not rounded subapical spot. For C.autumnalissp. nov., the apical lunula near the elytral suture is thickened but not linear and slender, and its elytra are more metallic brownish than those of C.pseudocylindriformis. Although their aedeagi characteristics are not distinctive, the body size of the proposed two new species is different. Field observation revealed that niche utilization would be relevant for differentiating these closely related species.
Collapse
Affiliation(s)
- Ming-Hsun Chou
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
| |
Collapse
|
5
|
Wallis GP, Jorge F. Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia. Mol Ecol 2018; 27:4368-4396. [DOI: 10.1111/mec.14875] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Gómez‐Rodríguez C, Timmermans MJTN, Crampton‐Platt A, Vogler AP. Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carola Gómez‐Rodríguez
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Departamento de Zoología Facultad de Biología Universidad de Santiago de Compostela c/Lope Gómez de Marzoa s/n Santiago de Compostela 15782 Spain
| | - Martijn J. T. N. Timmermans
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Natural Sciences Middlesex University Hendon Campus London NW4 4BT UK
| | - Alex Crampton‐Platt
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Genetics, Evolution and Environment University College London Gower Street London WC1E 6BT UK
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
| |
Collapse
|
8
|
Islands in the desert: Species delimitation and evolutionary history of Pseudotetracha tiger beetles (Coleoptera: Cicindelidae: Megacephalini) from Australian salt lakes. Mol Phylogenet Evol 2016; 101:279-285. [DOI: 10.1016/j.ympev.2016.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/09/2016] [Accepted: 05/16/2016] [Indexed: 11/19/2022]
|
9
|
Andújar C, Faille A, Pérez-González S, Zaballos JP, Vogler AP, Ribera I. Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles. Mol Phylogenet Evol 2016; 99:235-246. [DOI: 10.1016/j.ympev.2016.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
|
10
|
Wade EJ, Hertach T, Gogala M, Trilar T, Simon C. Molecular species delimitation methods recover most song‐delimited cicada species in the European
Cicadetta montana
complex. J Evol Biol 2015; 28:2318-36. [DOI: 10.1111/jeb.12756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/23/2015] [Accepted: 09/06/2015] [Indexed: 12/30/2022]
Affiliation(s)
- E. J. Wade
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
| | - T. Hertach
- Department of Environmental Sciences, Biogeography University of Basel Basel Switzerland
| | - M. Gogala
- Slovenian Academy of Sciences and Arts Ljubljana Slovenia
| | - T. Trilar
- Slovenian Museum of Natural History Ljubljana Slovenia
| | - C. Simon
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
- School of Biological Sciences Victoria University of Wellington Wellington New Zealand
| |
Collapse
|
11
|
Kekkonen M, Mutanen M, Kaila L, Nieminen M, Hebert PDN. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths. PLoS One 2015; 10:e0122481. [PMID: 25849083 PMCID: PMC4406103 DOI: 10.1371/journal.pone.0122481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/22/2015] [Indexed: 11/26/2022] Open
Abstract
The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.
Collapse
Affiliation(s)
- Mari Kekkonen
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Oulu, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
| | - Marko Nieminen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
12
|
López-López A, Abdul Aziz A, Galián J. Molecular phylogeny and divergence time estimation ofCosmodela(Coleoptera: Carabidae: Cicindelinae) tiger beetle species from Southeast Asia. ZOOL SCR 2015. [DOI: 10.1111/zsc.12113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alejandro López-López
- Departamento de Zoología y Antropología Física; Edificio Facultad de Veterinaria; 3ª Planta; Universidad de Murcia; Espinardo 30100 Murcia Spain
| | - Azidah Abdul Aziz
- Institute of Biological Sciences; Faculty of Science; University of Malaya; Kuala Lumpur 50603 Malaysia
| | - José Galián
- Departamento de Zoología y Antropología Física; Edificio Facultad de Veterinaria; 3ª Planta; Universidad de Murcia; Espinardo 30100 Murcia Spain
| |
Collapse
|
13
|
Goldberg J, Knapp M, Emberson RM, Townsend JI, Trewick SA. Species radiation of carabid beetles (broscini: mecodema) in new zealand. PLoS One 2014; 9:e86185. [PMID: 24465949 PMCID: PMC3900486 DOI: 10.1371/journal.pone.0086185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 12/06/2013] [Indexed: 11/29/2022] Open
Abstract
New Zealand biodiversity has often been viewed as Gondwanan in origin and age, but it is increasingly apparent from molecular studies that diversification, and in many cases origination of lineages, postdate the break-up of Gondwanaland. Relatively few studies of New Zealand animal species radiations have as yet been reported, and here we consider the species-rich genus of carabid beetles, Mecodema. Constrained stratigraphic information (emergence of the Chatham Islands) and a substitution rate for Coleoptera were separately used to calibrate Bayesian relaxed molecular clock date estimates for diversification of Mecodema. The inferred timings indicate radiation of these beetles no earlier than the mid-Miocene with most divergences being younger, dating to the Plio-Pleistocene. A shallow age for the radiation along with a complex spatial distribution of these taxa involving many instances of sympatry implicates recent ecological speciation rather than a simplistic allopatric model. This emphasises the youthful and dynamic nature of New Zealand evolution that will be further elucidated with detailed ecological and population genetic analyses.
Collapse
Affiliation(s)
- Julia Goldberg
- Department of Morphology, Systematics and Evolutionary Biology, J.F. Blumenbach Institute of Zoology & Anthropology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail:
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | | | - Steven A. Trewick
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| |
Collapse
|
14
|
Renner MA, Devos N, Patiño J, Brown EA, Orme A, Elgey M, Wilson TC, Gray LJ, von Konrat MJ. Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales, Jungermanniopsida), including two reinstated and five new species. PHYTOKEYS 2013; 27:1-113. [PMID: 24223490 PMCID: PMC3821098 DOI: 10.3897/phytokeys.27.5523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/20/2013] [Indexed: 05/11/2023]
Abstract
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.
Collapse
Affiliation(s)
- Matt A.M. Renner
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Nicolas Devos
- Department of Biology, Duke University, Box 90388, Durham NC 27708, U.S.A
| | - Jairo Patiño
- Institute of Botany, University of Liège, Liège, Belgium
| | - Elizabeth A. Brown
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Andrew Orme
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Michael Elgey
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Trevor C. Wilson
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Lindsey J. Gray
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia
| | - Matt J. von Konrat
- The Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois, USA
| |
Collapse
|
15
|
Talavera G, Dincă V, Vila R. Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12107] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Gerard Talavera
- Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra; Passeig Marítim de la Barceloneta, 37 08003 Barcelona Spain
| | - Vlad Dincă
- Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra; Passeig Marítim de la Barceloneta, 37 08003 Barcelona Spain
- Department of Zoology; Stockholm University; 10 691 Stockholm Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra; Passeig Marítim de la Barceloneta, 37 08003 Barcelona Spain
| |
Collapse
|
16
|
Fujisawa T, Barraclough TG. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol 2013; 62:707-24. [PMID: 23681854 PMCID: PMC3739884 DOI: 10.1093/sysbio/syt033] [Citation(s) in RCA: 838] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 11/19/2012] [Accepted: 05/03/2013] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
Collapse
Affiliation(s)
- Tomochika Fujisawa
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and Department of Entomology, Natural History Museum, London SW7 5BD, UK
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and Department of Entomology, Natural History Museum, London SW7 5BD, UK
| |
Collapse
|
17
|
Ratnasingham S, Hebert PDN. A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 2013; 8:e66213. [PMID: 23861743 PMCID: PMC3704603 DOI: 10.1371/journal.pone.0066213] [Citation(s) in RCA: 1034] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/08/2013] [Indexed: 11/30/2022] Open
Abstract
Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.
Collapse
|
18
|
Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus). Syst Biol 2013; 62:805-23. [PMID: 23771888 DOI: 10.1093/sysbio/syt041] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
Collapse
Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio University, Columbus, OH 43210, USA and Department of Biology, San Diego University, San Diego, CA 92182, USA
| | | | | |
Collapse
|
19
|
Parnmen S, Rangsiruji A, Mongkolsuk P, Boonpragob K, Nutakki A, Lumbsch HT. Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS One 2012; 7:e52245. [PMID: 23272229 PMCID: PMC3525555 DOI: 10.1371/journal.pone.0052245] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/16/2012] [Indexed: 11/17/2022] Open
Abstract
The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania.
Collapse
Affiliation(s)
- Sittiporn Parnmen
- Department of Biology, Srinakharinwirot University, Bangkok, Thailand
- Department of Biology, Ramkhamhaeng University, Bangkok, Thailand
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
| | | | | | | | - Aparna Nutakki
- Department of Biological Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Botany Department, The Field Museum, Chicago, Illinois, United States of America
| |
Collapse
|
20
|
Reid NM, Carstens BC. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol 2012; 12:196. [PMID: 23031350 PMCID: PMC3503838 DOI: 10.1186/1471-2148-12-196] [Citation(s) in RCA: 329] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities. Results We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits. Conclusion Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors’ websites.
Collapse
Affiliation(s)
- Noah M Reid
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | |
Collapse
|
21
|
Marshall DC, Hill KBR, Marske KA, Chambers C, Buckley TR, Simon C. Limited, episodic diversification and contrasting phylogeography in a New Zealand cicada radiation. BMC Evol Biol 2012; 12:177. [PMID: 22967046 PMCID: PMC3537654 DOI: 10.1186/1471-2148-12-177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 08/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The New Zealand (NZ) cicada fauna contains two co-distributed lineages that independently colonized the isolated continental fragment in the Miocene. One extensively studied lineage includes 90% of the extant species (Kikihia + Maoricicada + Rhodopsalta; ca 51 spp.), while the other contains just four extant species (Amphipsalta - 3 spp. + Notopsalta - 1 sp.) and has been little studied. We examined mitochondrial and nuclear-gene phylogenies and phylogeography, Bayesian relaxed-clock divergence timing (incorporating literature-based uncertainty of molecular clock estimates) and ecological niche models of the species from the smaller radiation. RESULTS Mitochondrial and nuclear-gene trees supported the monophyly of Amphipsalta. Most interspecific diversification within Amphipsalta-Notopsalta occurred from the mid-Miocene to the Pliocene. However, interspecific divergence time estimates had large confidence intervals and were highly dependent on the assumed tree prior, and comparisons of uncorrected and patristic distances suggested difficulty in estimation of branch lengths. In contrast, intraspecific divergence times varied little across analyses, and all appear to have occurred during the Pleistocene. Two large-bodied forest taxa (A. cingulata, A. zelandica) showed minimal phylogeographic structure, with intraspecific diversification dating to ca. 0.16 and 0.37 Ma, respectively. Mid-Pleistocene-age phylogeographic structure was found within two smaller-bodied species (A. strepitans - 1.16 Ma, N. sericea - 1.36 Ma] inhabiting dry open habitats. Branches separating independently evolving species were long compared to intraspecific branches. Ecological niche models hindcast to the Last Glacial Maximum (LGM) matched expectations from the genetic datasets for A. zelandica and A. strepitans, suggesting that the range of A. zelandica was greatly reduced while A. strepitans refugia were more extensive. However, no LGM habitat could be reconstructed for A. cingulata and N. sericea, suggesting survival in microhabitats not detectable with our downscaled climate data. CONCLUSIONS Unlike the large and continuous diversification exhibited by the Kikihia-Maoricicada-Rhodopsalta clade, the contemporaneous Amphipsalta-Notopsalta lineage contains four comparatively old (early branching) species that show only recent diversification. This indicates either a long period of stasis with no speciation, or one or more bouts of extinction that have pruned the radiation. Within Amphipsalta-Notopsalta, greater population structure is found in dry-open-habitat species versus forest specialists. We attribute this difference to the fact that NZ lowland forests were repeatedly reduced in extent during glacial periods, while steep, open habitats likely became more available during late Pleistocene uplift.
Collapse
Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Katharine A Marske
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
- Landcare Research, Private Bag 92170, Auckland, New Zealand
| | - Colleen Chambers
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd, Storrs, CT, 06269, USA
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| |
Collapse
|
22
|
The Invertebrate Life of New Zealand: A Phylogeographic Approach. INSECTS 2011; 2:297-325. [PMID: 26467729 PMCID: PMC4553545 DOI: 10.3390/insects2030297] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/16/2011] [Accepted: 06/17/2011] [Indexed: 11/17/2022]
Abstract
Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand's invertebrates.
Collapse
|
23
|
Marske KA, Leschen RA, Buckley TR. Reconciling phylogeography and ecological niche models for New Zealand beetles: Looking beyond glacial refugia. Mol Phylogenet Evol 2011; 59:89-102. [DOI: 10.1016/j.ympev.2011.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 11/12/2010] [Accepted: 01/13/2011] [Indexed: 02/07/2023]
|