Journal articles: 'Species delimitation methods'

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O'Meara, Brian C. "New Heuristic Methods for Joint Species Delimitation and Species Tree Inference." Systematic Biology 59, no. 1 (November 10, 2009): 59–73. http://dx.doi.org/10.1093/sysbio/syp077.

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Rannala, Bruce. "The art and science of species delimitation." Current Zoology 61, no. 5 (October 1, 2015): 846–53. http://dx.doi.org/10.1093/czoolo/61.5.846.

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Abstract DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the framework of the multi-species coalescent (MSC). In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation (and their limitations) are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today’s technologies.

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Tuovila, Hanna, and Seppo Huhtinen. "New methods for mycocalicioid fungi." Lichenologist 52, no. 6 (November 2020): 403–13. http://dx.doi.org/10.1017/s0024282920000481.

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AbstractThe identification of mycocalicioid species continues to be based on morphological and chemical characters, even though molecular data and substratum preferences can provide many important insights into specific problems associated with species delimitation and other taxonomic challenges. Our results reinforce the usefulness of many morphological and chemical characteristics and reveal several new features that can be used for both species delimitation and identification. Given the fact that mycocalicioid species can rarely be distinguished by just a single character, combinations of different chemical and morphological characteristics must be used. Additional characteristics must also be sought, including those that have previously been overlooked or still need to be discovered. As a result of this search, we introduce a new term, pseudohemiamyloid, for a reversible, KOH resistant/enhanced reaction in Lugol's solution.

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Campillo, Luke C., Anthony J. Barley, and Robert C. Thomson. "Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?" Systematic Biology 69, no. 4 (December 16, 2019): 708–21. http://dx.doi.org/10.1093/sysbio/syz072.

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Abstract A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

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Košuthová, Alica, Martin Westberg, Mónica A. G. Otálora, and Mats Wedin. "Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes)." MycoKeys 47 (February 20, 2019): 17–33. http://dx.doi.org/10.3897/mycokeys.47.32227.

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Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostaniacoccophylla, R.paramensis, R.quadrifida) are excluded and transferred to other genera. Rostaniaoccultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogiumparamense and Scytiniumquadrifidum are proposed.

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Edwards, Danielle L., and L. Lacey Knowles. "Species detection and individual assignment in species delimitation: can integrative data increase efficacy?" Proceedings of the Royal Society B: Biological Sciences 281, no. 1777 (February 22, 2014): 20132765. http://dx.doi.org/10.1098/rspb.2013.2765.

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Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

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Özgişi, Kurtuluş, Burcu Tarıkahya-Hacıoğlu, and Atilla Ocak. "Species delimitation in Noccaea densiflora species complex (Brassicaceae) based on morphological and molecular data." Botany 99, no. 7 (July 2021): 389–402. http://dx.doi.org/10.1139/cjb-2020-0184.

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The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. Nuclear ribosomal internal transcribed spacer, chloroplast trnL-F, and trnQ-5′rps16 regions were used for species delimitation using the multispecies coalescent model as implemented in two developed Bayesian methods. Internal transcribed spacer and trnL-F regions were also used for Templeton, Crandall, and Singh haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on the analyses, it was determined that only one population of N. densiflora (Boiss. & Kotschy) F.K. Mey. and one of Noccaea microstyla (Boiss.) F.K. Mey. were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.

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Lu, Zhiqiang, Yongshuai Sun, Ying Li, Yongzhi Yang, Gaini Wang, and Jianquan Liu. "Species delimitation and hybridization history of a hazel species complex." Annals of Botany 127, no. 7 (February 10, 2021): 875–86. http://dx.doi.org/10.1093/aob/mcab015.

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Abstract Background and Aims Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis–Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. Methods A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. Key Results Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. Conclusions Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.

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Lim, Gwynne S., Michael Balke, and Rudolf Meier. "Determining Species Boundaries in a World Full of Rarity: Singletons, Species Delimitation Methods." Systematic Biology 61, no. 1 (April 11, 2011): 165–69. http://dx.doi.org/10.1093/sysbio/syr030.

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Haelewaters, D., and D. H. Pfister. "Morphological Species of Gloeandromyces (Ascomycota, Laboulbeniales) Evaluated Using Single-locus Species Delimitation Methods." Fungal Systematics and Evolution 3, no. 1 (June 15, 2019): 19–34. http://dx.doi.org/10.3114/fuse.2019.03.03.

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Nadler, Steven. "Species delimitation and nematode biodiversity: phylogenies rule." Nematology 4, no. 5 (2002): 615–25. http://dx.doi.org/10.1163/15685410260438908.

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AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

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PINO-BODAS, Raquel, Ana Rosa BURGAZ, Teuvo AHTI, and Soili STENROOS. "Taxonomy ofCladonia angustilobaand related species." Lichenologist 50, no. 3 (May 2018): 267–82. http://dx.doi.org/10.1017/s002428291800018x.

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AbstractThe lichen speciesCladonia angustilobais characterized by a well-developed primary thallus and narrow squamules which show deep incisions, and the presence of usnic and fumarprotocetraric acids. Morphologically it is similar toC. foliaceaandC. convoluta, from which it can be distiguished by the squamule size and morphology. Since similar characters were used to distinguishC. foliaceafromC. convolutawhich do not represent different lineages, it is necessary to examine the taxonomic status ofC. angustilobaby means of DNA sequences. In this study, the species delimitation within theC. foliaceacomplex was studied by sequencing three loci, ITS rDNA,cox1andRPB2. The data were analyzed by means of phylogenetic and species delimitation methods (GMYC, PTP, ABGD and BPP). Our results show that none of the three species is monophyletic. Most of the species delimitation methods did not support the current species as evolutionary lineages. Only some of the BPP analyses supportedC. angustilobaas a species distinct fromC. foliaceaandC. convoluta. However, the hypothesis that considers theC. foliaceacomplex as constituted by a unique species obtained the best Bayes Factor value. Therefore,C. angustilobaandC. convolutaare synonymized withC. foliacea.A new, thoroughly checked synonymy with typifications of the wholeC. foliaceacomplex is presented. An updated survey of the world distribution data is compiled.

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Afonso Silva, Ana C., Natali Santos, Huw A. Ogilvie, and Craig Moritz. "Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology." PeerJ 5 (August 29, 2017): e3724. http://dx.doi.org/10.7717/peerj.3724.

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While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species ofCarliaskinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia,Carlia johnstoneiandC. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genusCarlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identifiedCarlialineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not requirea prioriresolved species or gene trees. Compared to the situation inC. triacantha, morphological divergence was greater between the two lineages within Kimberley endemicC. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species withinC. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespreadC. triacantha. With this work, we describe two new species,Carlia insularissp. nov andCarlia isostriacanthasp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.

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Wade, E. J., T. Hertach, M. Gogala, T. Trilar, and C. Simon. "Molecular species delimitation methods recover most song-delimited cicada species in the EuropeanCicadetta montanacomplex." Journal of Evolutionary Biology 28, no. 12 (November 3, 2015): 2318–36. http://dx.doi.org/10.1111/jeb.12756.

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Singh, Sohana P., Johan C. Groeneveld, Abdulaziz Al-Marzouqi, and Sandi Willows-Munro. "A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean." PeerJ 5 (May 25, 2017): e3356. http://dx.doi.org/10.7717/peerj.3356.

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Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

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Muñoz-Tobar, Sofía, and Michael Caterino. "Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes." Insects 11, no. 1 (January 20, 2020): 64. http://dx.doi.org/10.3390/insects11010064.

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The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

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Becchimanzi, Andrea, Beata Zimowska, and Rosario Nicoletti. "Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses." Pathogens 10, no. 9 (September 10, 2021): 1167. http://dx.doi.org/10.3390/pathogens10091167.

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Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. cladosporioides, we tested four methods of species delimitation using the combined DNA barcodes internal transcribed spacers, translation elongation factor 1-α and actin 1. The analyses involved 105 isolates, revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we found that eight isolates from this set should be ascribed to Cladosporium anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches in order to minimize the risk of considering false positives.

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Giarla, Thomas C., Robert S. Voss, and Sharon A. Jansa. "Hidden diversity in the Andes: Comparison of species delimitation methods in montane marsupials." Molecular Phylogenetics and Evolution 70 (January 2014): 137–51. http://dx.doi.org/10.1016/j.ympev.2013.09.019.

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da Silva, Raimundo, Pedro L. V. Peloso, Marcelo José Sturaro, Ivana Veneza, Iracilda Sampaio, Horacio Schneider, and Grazielle Gomes. "Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae)." Mitochondrial DNA Part A 29, no. 7 (December 7, 2017): 1108–14. http://dx.doi.org/10.1080/24701394.2017.1413364.

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Luo, Arong, Cheng Ling, Simon Y. W. Ho, and Chao-Dong Zhu. "Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios." Systematic Biology 67, no. 5 (February 15, 2018): 830–46. http://dx.doi.org/10.1093/sysbio/syy011.

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de Jesus, Priscila Barreto, Adriele Leite Costa, José Marcos de Castro Nunes, Antonio Manghisi, Giuseppa Genovese, Marina Morabito, and Alessandra Selbach Schnadelbach. "Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae, Rhodophyta)." European Journal of Phycology 54, no. 2 (December 17, 2018): 135–53. http://dx.doi.org/10.1080/09670262.2018.1522454.

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Lecocq, Thomas, Simon Dellicour, Denis Michez, Manuel Dehon, Alexandre Dewulf, Thibaut De Meulemeester, Nicolas Brasero, Irena Valterová, Jean-Yves Rasplus, and Pierre Rasmont. "Methods for species delimitation in bumblebees (Hymenoptera, Apidae,Bombus): towards an integrative approach." Zoologica Scripta 44, no. 3 (February 27, 2015): 281–97. http://dx.doi.org/10.1111/zsc.12107.

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Miralles, Aurélien, Jörn Köhler, Frank Glaw, and Miguel Vences. "Species delimitation methods put into taxonomic practice: two new Madascincus species formerly allocated to historical species names (Squamata, Scincidae)." Zoosystematics and Evolution 92, no. 2 (December 6, 2016): 257–75. http://dx.doi.org/10.3897/zse.92.9945.

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Sukumaran, Jeet, and L. Lacey Knowles. "Multispecies coalescent delimits structure, not species." Proceedings of the National Academy of Sciences 114, no. 7 (January 30, 2017): 1607–12. http://dx.doi.org/10.1073/pnas.1607921114.

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The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.

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Huang, Jun, Tomáš Flouri, and Ziheng Yang. "A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model." Molecular Biology and Evolution 37, no. 11 (July 8, 2020): 3211–24. http://dx.doi.org/10.1093/molbev/msaa166.

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Abstract We use computer simulation to examine the information content in multilocus data sets for inference under the multispecies coalescent model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes, and cross-species introgression probabilities), species tree estimation, and species delimitation based on Bayesian comparison of delimitation models. We found that the number of loci is the most influential factor for almost all inference problems examined. Although the number of sequences per species does not appear to be important to species tree estimation, it is very influential to species delimitation. Increasing the number of sites and the per-site mutation rate both increase the mutation rate for the whole locus and these have the same effect on estimation of parameters, but the sequence length has a greater effect than the per-site mutation rate for species tree estimation. We discuss the computational costs when the data size increases and provide guidelines concerning the subsampling of genomic data to enable the application of full-likelihood methods of inference.

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Martinsson, Svante, and Christer Erséus. "Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview." Diversity 13, no. 2 (January 20, 2021): 36. http://dx.doi.org/10.3390/d13020036.

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Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

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Martínez-Arce, Arely, Alberto De Jesús-Navarrete, and Francesca Leasi. "DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species." Diversity 12, no. 3 (March 19, 2020): 107. http://dx.doi.org/10.3390/d12030107.

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Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

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Fernández, Rosa, and Gonzalo Giribet. "Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi)." Invertebrate Systematics 28, no. 4 (2014): 401. http://dx.doi.org/10.1071/is14009.

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Aoraki denticulata, a widespread mite harvestman endemic to the NW South Island of New Zealand, was postulated to constitute an old lineage with deep genetic history. Expanding on previous studies, we explored its genetic diversity and population structure, phylogeography and diversification patterns. We also examined the systematic implications of such a complex scenario through species delimitation analyses under coalescent-based and barcoding gap discovery methodologies. Our results depict the deep evolutionary history of the A. denticulata lineage, which shows high geographic structure and low genetic connectivity among modern populations. Aoraki denticulata is further subdivided into three lineages: a lineage presently inhabiting the northern region of the Southern Alps (and including the subspecies A. d. major), a second lineage in the north-eastern part of the sampled land, and a third one occupying the south-eastern localities. When using species delimitation methods based on coalescence approaches, large numbers of cryptic species were estimated. Based on morphological and biological evidence, we thus argue that these methods may overestimate species in cases in which genetic divergence is unusually large and discuss the systematic implications of our findings.

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Rojas, Rommel R., Antoine Fouquet, Santiago R. Ron, Emil José Hernández-Ruz, Paulo R. Melo-Sampaio, Juan C. Chaparro, Richard C. Vogt, et al. "A Pan-Amazonian species delimitation: high species diversity within the genusAmazophrynella(Anura: Bufonidae)." PeerJ 6 (July 9, 2018): e4941. http://dx.doi.org/10.7717/peerj.4941.

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Amphibians are probably the most vulnerable group to climate change and climate-change associate diseases. This ongoing biodiversity crisis makes it thus imperative to improve the taxonomy of anurans in biodiverse but understudied areas such as Amazonia. In this study, we applied robust integrative taxonomic methods combining genetic (mitochondrial 16S, 12S and COI genes), morphological and environmental data to delimit species of the genusAmazophrynella(Anura: Bufonidae) sampled from throughout their pan-Amazonian distribution. Our study confirms the hypothesis that the species diversity of the genus is grossly underestimated. Our analyses suggest the existence of eighteen linages of which seven are nominal species, three Deep Conspecific Lineages, one Unconfirmed Candidate Species, three Uncategorized Lineages, and four Confirmed Candidate Species and described herein. We also propose a phylogenetic hypothesis for the genus and discuss its implications for historical biogeography of this Amazonian group.

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Valdez-Mondragón, Alejandro, Claudia I. Navarro-Rodríguez, Karen P. Solís-Catalán, Mayra R. Cortez-Roldán, and Alma R. Juárez-Sánchez. "Under an integrative taxonomic approach: the description of a new species of the genus Loxosceles (Araneae, Sicariidae) from Mexico City." ZooKeys 892 (November 27, 2019): 93–133. http://dx.doi.org/10.3897/zookeys.892.39558.

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A new species of the spider genus Loxosceles Heineken & Lowe, 1832, Loxosceles tenochtitlan Valdez-Mondragón & Navarro-Rodríguez, sp. nov., is described based on adult male and female specimens from the states of Mexico City, Estado de Mexico and Tlaxcala. Integrative taxonomy including traditional morphology, geometric and lineal morphology, and molecules (DNA barcodes of cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2)), were used as evidence to delimit the new species. Four methods were used for molecular analyses and species delimitation: 1) corrected p-distances under neighbor joining (NJ), 2) automatic barcode gap discovery (ABGD), 3) general mixed yule coalescent model (GMYC), and 4) poisson tree processes (bPTP). All molecular methods, traditional, geometric and lineal morphology were consistent in delimiting and recognizing the new species. Loxosceles tenochtitlansp. nov. is closely related to L. misteca based on molecular data. Although both species are morphologically similar, the average p-distance from CO1 data was 13.8% and 4.2% for ITS2 data. The molecular species delimitation methods recovered well-supported monophyletic clusters for samples of L. tenochtitlansp. nov. from Mexico City + Tlaxcala and for samples of L. misteca from Guerrero. Loxosceles tenochtitlansp. nov. is considered a unique species for three reasons: (1) it can be distinguished by morphological characters (genitalic and somatic); (2) the four different molecular species delimitation methods were congruent to separate both species; and (3) there is variation in leg I length of males between both species, with the males of L. misteca having longer legs than males of L. tenochtitlansp. nov., also morphometrically, the shape of tibiae of the palp between males of both species is different.

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DeSalle, Rob, Mary G. Egan, and Mark Siddall. "The unholy trinity: taxonomy, species delimitation and DNA barcoding." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (September 14, 2005): 1905–16. http://dx.doi.org/10.1098/rstb.2005.1722.

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Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this ‘DNA barcoding’ initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the ‘DNA barcoding’ initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the ‘DNA barcoding’ initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings—Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of ‘DNA barcoding’.

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Yusseff-Vanegas, Sohath Z., and Ingi Agnarsson. "DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region." PeerJ 5 (July 25, 2017): e3516. http://dx.doi.org/10.7717/peerj.3516.

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Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation forLucilia eximia, Lucilia retroversa, Lucilia ricaandChloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

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Blair, Christopher, and Robert W. Bryson. "Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae:Phrynosoma)." Molecular Ecology Resources 17, no. 6 (February 27, 2017): 1168–82. http://dx.doi.org/10.1111/1755-0998.12658.

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Torrano-Silva, Beatriz N., Bruno R. Vieira, Rafael Riosmena-Rodríguez, and Mariana C. Oliveira. "Guidelines for DNA barcoding of coralline algae, focusing on Lithophylloideae (Corallinales) from Brazil." Botanica Marina 61, no. 2 (March 28, 2018): 127–40. http://dx.doi.org/10.1515/bot-2017-0040.

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AbstractMultiple-marker (COI-5P, UPA,psbA andrbcL-3P) and two algorithmic approaches [automatic barcode gap discovery (ABGD) and Poisson tree process (PTP)] were used for species delimitation of Lithophylloideae in Brazil. The integrative approach was mostly congruent between markers and algorithmic methods of species delimitation, suggesting the occurrence of 24 species. Based on morphology and molecular data,Amphiroa rigida,Amphiroa vanbosseae,Lithophyllum atlanticum,Lithophyllum kaiseri,Lithophyllum margaritae,Titanoderma pustulatum,Titanoderma prototypumandPaulsilvella huveorum, which were previously reported for Brazil, are confirmed in this work. Six new species are distinguished by both molecular and morphological traits, and they are provisionally named asAmphiroasp. 1,Amphiroasp. 2,Amphiroasp. 3,Lithophyllumsp. 1,Lithophyllumsp. 2 andLithophyllumsp. 3. Another 10 species are cryptic and cannot be distinguished based on traditionally used morphological traits. These includeAmphiroasp. 4,Lithophyllumsp. 4, three species that are morphologically named underAmphiroa beauvoisii, and six that share the morphology described forAmphiroa fragilissima. All four markers used were useful for species delimitation. However, a combination of practical aspects and levels of intra- and interspecific divergence values led us to propose the use ofrbcL-3P as a standard DNA barcode marker for the Corallinales.

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Amador, Luis, Andrés Parada, Guillermo D’Elía, and Juan M. Guayasamin. "Uncovering hidden specific diversity of Andean glassfrogs of theCentrolene buckleyispecies complex (Anura: Centrolenidae)." PeerJ 6 (October 31, 2018): e5856. http://dx.doi.org/10.7717/peerj.5856.

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The glassfrogCentrolene buckleyihas been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized asC. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in theC. buckleyispecies complex. Finally, our results support the validity ofC. venezuelense, formerly considered as a subspecies ofC. buckleyi.

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Ruiz-Sanchez, Eduardo. "Parametric and non-parametric species delimitation methods result in the recognition of two new Neotropical woody bamboo species." Molecular Phylogenetics and Evolution 93 (December 2015): 261–73. http://dx.doi.org/10.1016/j.ympev.2015.08.004.

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Postaire, Bautisse, Hélène Magalon, Chloé A. F. Bourmaud, and J. Henrich Bruggemann. "Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa)." Molecular Phylogenetics and Evolution 105 (December 2016): 36–49. http://dx.doi.org/10.1016/j.ympev.2016.08.013.

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Li, Meng, Qiongyao Zhao, Rong Chen, Jiajun He, Tao Peng, Wenbo Deng, Yanli Che, and Zongqing Wang. "Species diversity revealed in Sigmella Hebard, 1929 (Blattodea, ectobiidae) based on morphology and four molecular species delimitation methods." PLOS ONE 15, no. 6 (June 10, 2020): e0232821. http://dx.doi.org/10.1371/journal.pone.0232821.

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EVANGELISTA, DOMINIC A., GODFREY BOURNE, and JESSICA L. WARE. "Species richness estimates of Blattodea s.s. (Insecta: Dictyoptera) from northern Guyana vary depending upon methods of species delimitation." Systematic Entomology 39, no. 1 (November 5, 2013): 150–58. http://dx.doi.org/10.1111/syen.12043.

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Ottoni, Felipe Polivanov, José L. O. Mattos, Axel M. Katz, and Pedro H. N. Bragança. "Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments." Zoosystematics and Evolution 95, no. 1 (February 13, 2019): 49–64. http://dx.doi.org/10.3897/zse.95.31658.

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Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, and we considered the possibility of two slightly variant scenarios. A time-calibrated phylogenetic analysis is proposed based on the predominant congruence of the results of these three species delimitation methods herein applied. The monophyly of theA.autranispecies group was highly supported with maximum node support value and diagnosed by 11 nucleotide substitutions. The sister clade of theA.autranispecies group is the clade comprisingA.sp. Timbé do Sul andA.minuano. The phylogenetic analysis supports three main clades within theA.autranispecies group, supported by maximum node support value, with the Southern Mata Atlântica clade as the most basal clade. Divergence time estimates indicate that the diversification of theAustraloherosoriginated during the early Neogene, but only in the late Neogene did the processes of diversification in the southeast and north regions occur. Diversification within theAustraloherosautranispecies group occurred synchronically for the three main clades during the beginning of the Quaternary. It is demonstrated that molecular characters are valuable tools for species recognition, particularly in speciose groups with inconspicuous or difficult to record morphological characters. The resulting phylogeny of theAustraloherosautranigroup is highly compatible with the geological and biogeographic scenarios proposed for the Neogene and Quarternary shaping of the extant river basins of eastern Brazil. Despite the origin of theA.autranigroup being dated to the late Miocene, species level diversification occurred in the Pleistocene and was probably driven by headwater capture events and sea-level fluctuations.

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Santos, Allan P. M., Daniela M. Takiya, and Jorge L. Nessimian. "Integrative taxonomy ofMetrichiaRoss (Trichoptera: Hydroptilidae: Ochrotrichiinae) microcaddisflies from Brazil: descriptions of twenty new species." PeerJ 4 (May 5, 2016): e2009. http://dx.doi.org/10.7717/peerj.2009.

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Metrichiais assigned to the Ochrotrichiinae, a group of almost exclusively Neotropical microcaddisflies.Metrichiacomprises over 100 described species and, despite its diversity, only one species has been described from Brazil so far. In this paper, we provide descriptions for 20 new species from 8 Brazilian states:M. acuminatasp. nov.,M. azulsp. nov.,M. bonitasp. nov.,M. bracuisp. nov.,M. caracasp. nov.,M. circuliformesp. nov.,M. curtasp. nov.,M. farofasp. nov.,M. forcepssp. nov.,M. formosinhasp. nov.,M. goianasp. nov.,M. itabaianasp. nov.,M. longissimasp. nov.,M. peludasp. nov.,M. rafaelisp. nov.,M. simplessp. nov.,M. talhadasp. nov.,M. teresp. nov.,M. ubajarasp. nov., andM. vulgarissp. nov.DNA barcode sequences (577 bp of the mitochondrial gene COI) were generated for 13 of the new species and two previously known species ofMetrichiaresulting in 64 sequences. In addition, COI sequences were obtained for other genera of Ochrotrichiinae (Angrisanoia,Nothotrichia,Ochrotrichia,Ragatrichia, andRhyacopsyche). DNA sequences and morphological data were integrated to evaluate species delimitations. K2P pairwise distances were calculated to generate a neighbor-joining tree. COI sequences also were submitted to ABGD and GMYC methods to assess ‘potential species’ delimitation. Analyses showed a conspicuous barcoding gap amongMetrichiasequences (highest intraspecific divergence: 4.8%; lowest interspecific divergence: 12.6%). Molecular analyses also allowed the association of larvae and adults ofMetrichia bonitasp. nov.from Mato Grosso do Sul, representing the first record of microcaddisfly larvae occurring in calcareous tufa (or travertine). ABGD results agreed with the morphological delimitation ofMetrichiaspecies, while GMYC estimated a slightly higher number of species, suggesting the division of two morphological species, each one into two potential species. Because this could be due to unbalanced sampling and the lack of morphological diagnostic characters, we have maintained these two species as undivided.

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Dahruddin, Hadi, Arni Sholihah, Tedjo Sukmono, Sopian Sauri, Ujang Nurhaman, Daisy Wowor, Dirk Steinke, and Nicolas Hubert. "Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods." Diversity 13, no. 7 (June 23, 2021): 283. http://dx.doi.org/10.3390/d13070283.

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Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

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Shirley, Matthew H., Kent A. Vliet, Amanda N. Carr, and James D. Austin. "Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation." Proceedings of the Royal Society B: Biological Sciences 281, no. 1776 (February 7, 2014): 20132483. http://dx.doi.org/10.1098/rspb.2013.2483.

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Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile ( Mecistops cataphractus ) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5–7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.

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Agüero-Chapin, Guillermin, Yuliana Jiménez, Aminael Sánchez-Rodríguez, Reinaldo Molina-Ruiz, Oscar Vivanco, and Agostinho Antunes. "DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics." Current Topics in Medicinal Chemistry 21, no. 7 (April 26, 2021): 599–611. http://dx.doi.org/10.2174/1568026621666210113164605.

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Background: Molecular phylogenetic algorithms frequently disagree with the approaches considering reproductive compatibility and morphological criteria for species delimitation. The question stems if the resulting species boundaries from molecular, reproductive and/or morphological data are definitively not reconcilable; or if the existing phylogenetic methods are not sensitive enough to agree morphological and genetic variation in species delimitation. Objectives : We propose DISTATIS as an integrative framework to combine alignment-based (AB) and alignment-free (AF) distance matrices from ITS2 sequences/structures to shed light whether Gelasinospora and Neurospora are sister but independent genera. Methods: We aimed at addressing this standing issue by harmonizing genus-specific classification based on their ascospore morphology and ITS2 molecular data. To validate our proposal, three phylogenetic approaches: i) traditional alignment-based, ii) alignment-free and iii) novel distance integrative (DI)-based were comparatively evaluated on a set of Gelasinospora and Neurospora species. All considered species have been extensively characterized at both the morphological and reproductive levels and there are known incongruences between their ascospore morphology and molecular data that hampers genus-specific delimitation. Results: Traditional AB phylogenetic analyses fail at resolving the Gelasinospora and Neurospora genera into independent monophyletic clades following ascospore morphology criteria. In contrast, AF and DI approaches produced phylogenetic trees that could properly delimit the expected monophyletic clades. Conclusions: The DI approach outperformed the AF one in the sense that it could also divide the Neurospora species according to their reproduction mode.

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ZIMMERMANN, BIANCA LAÍS, IVANKLIN SOARES CAMPOS-FILHO, GIOVANNA MONTICELLI CARDOSO, SANDRO SANTOS, JOSÉ OTÁVIO AGUIAR, and PAULA BEATRIZ ARAUJO. "Two new species of Atlantoscia Ferrara & Taiti, 1981 (Isopoda: Oniscidea: Philosciidae) from southern Brazil described in the light of integrative taxonomy." Zootaxa 4482, no. 3 (September 19, 2018): 551. http://dx.doi.org/10.11646/zootaxa.4482.3.7.

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The use of molecular data in association with classical taxonomy has helped to alleviate the taxonomic impediment through the discovery, delimitation and description of new species. Terrestrial isopods are the largest suborder of Isopoda; however, there are very few active taxonomists in this group and a representative part of the terrestrial isopods world diversity remains unexplored. The genus Atlantoscia comprises five species in which diagnostic characters are few and show subtle differences among the species. The objective of this study was to delimit and describe two new species of the genus Atlantoscia from southern Brazil by using traditional taxonomy coupled with genetic information. Specimens were analyzed morphologically and by the aid of two molecular markers, mitochondrial COI and nuclear 18S rRNA. The validity of the new species Atlantoscia antennamaculata sp. nov. and Atlantoscia australis sp. nov. was corroborated, unambiguously, by morphological approach, phylogenetic analysis and species delimitation methods. Our study reinforces the fact that, despite the undeniable importance of comparative morphology in species discovery, new methods and data, particularly molecular ones, are becoming prominent and an integrative part of the taxonomy practice.

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Bustamante, Danilo E., Manuel Oliva, Santos Leiva, Jani E. Mendoza, Leidy Bobadilla, Geysen Angulo, and Martha S. Calderon. "Phylogeny and species delimitations in the entomopathogenic genus Beauveria (Hypocreales, Ascomycota), including the description of B. peruviensis sp. nov." MycoKeys 58 (September 9, 2019): 47–68. http://dx.doi.org/10.3897/mycokeys.58.35764.

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The genus Beauveria is considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species. Species identification in Beauveria is difficult because of its structural simplicity and the lack of distinctive phenotypic variation. Therefore, the use of multi-locus sequence data is essential to establish robust species boundaries in addition to DNA-based species delimitation methods using genetic distance, coalescent, and genealogical concordance approaches (polyphasic approaches). In this regard, our study used multilocus phylogeny and five DNA-based methods to delimit species in Beauveria using three molecular makers. These polyphasic analyses allowed for the delimitation of 20–28 species in Beauveria, confirming cryptic diversity in five species (i.e. B. amorpha, B. bassiana, B. diapheromeriphila, and B. pseudobassiana) and supporting the description of B. peruviensis as a new taxon from northeastern Peru. The other five species were not evaluated as they did not have enough data (i.e. B. araneola, B. gryllotalpidicola, B. loeiensis, B. medogensis, and B. rudraprayagi). Our results demonstrate that the congruence among different methods in a polyphasic approach (e.g. genetic distance and coalescence methods) is more likely to show reliably supported species boundaries. Among the methods applied in this study, genetic distance, coalescent approaches, and multilocus phylogeny are crucial when establishing species boundaries in Beauveria.

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Kara, Jyothi, Angus H. H. Macdonald, and Carol A. Simon. "Integrative taxonomic methods reveal an incorrect synonymisation of the South African Pseudonereis podocirra (Schmarda) as the widespread Pseudonereis variegata (Grube) from Chile." Invertebrate Systematics 32, no. 6 (2018): 1282. http://dx.doi.org/10.1071/is18016.

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The nereidid Pseudonereis variegata (Grube, 1866) described from Chile includes 14 synonymised species from 10 type localities with a discontinuous distribution, but no taxonomic or molecular studies have investigated the status of this species outside Chile. Two synonymised species, Mastigonereis podocirra Schmarda, 1861 and Nereis (Nereilepas) stimpsonis Grube, 1866, were described from South Africa and investigated here using morphological examination. MtCOI species delimitation analyses and morphology were used to determine the status of P. variegata in South Africa. Morphological examination revealed that museum and freshly collected specimens from South Africa that conform to the general description of P. variegata are similar to M. podocirra and N. stimpsonis with respect to the consistent absence of homogomph spinigers in the inferior neuropodial fascicle, expanded notopodial ligules and the subterminal attachment of dorsal cirri in posterior parapodia. The synonymy of M. podocirra and N. stimpsonis as P. variegata are rejected and P. podocirra, comb. nov. is reinstated. Morphologically, Pseudonereis podocirra differed from specimens from Chile with regard to the numbers of paragnaths, the absence of homogomph spinigers and changes in parapodial morphology along the body. Independence of these species was further supported by genetic distances, automatic barcode gap discovery and multi-rate Poisson tree process species delimitation analyses of 77 mtCOI sequences. Haplotype network revealed no genetic structuring within the South African populations. http://zoobank.org/urn:lsid:zoobank.org:pub:F0B1A5AF-9CE9-4A43-ACCF-17117E1C2F21

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Gélin, P., B. Postaire, C. Fauvelot, and H. Magalon. "Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites." Molecular Phylogenetics and Evolution 109 (April 2017): 430–46. http://dx.doi.org/10.1016/j.ympev.2017.01.018.

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Sagorny, Christina, Carina Wesseler, Daria Krämer, and Jörn von Döhren. "Assessing the diversity and distribution of Cephalothrix species (Nemertea: Palaeonemertea) in European waters by comparing different species delimitation methods." Journal of Zoological Systematics and Evolutionary Research 57, no. 3 (February 13, 2019): 497–519. http://dx.doi.org/10.1111/jzs.12266.

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Prévot, Vanya, Kurt Jordaens, Gontran Sonet, and Thierry Backeljau. "Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)." PLoS ONE 8, no. 4 (April 5, 2013): e60736. http://dx.doi.org/10.1371/journal.pone.0060736.

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Journal articles on the topic 'Species delimitation methods'

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