The importance of adopting an integrative taxonomy framework in species delimitation: Response to Hunter et al. (2021)

Ostrich ◽  
2021 ◽  
pp. 1-6
Author(s):  
Tshifhiwa G Mandiwana-Neudani ◽  
Timothy M Crowe ◽  
Robin M Little ◽  
Rauri CK Bowie
Keyword(s):  
Species Delimitation ◽  
Integrative Taxonomy

scholarly journals Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 428
Author(s):  
Martin Stervander ◽  
Bengt Hansson ◽  
Urban Olsson ◽  
Mark F. Hulme ◽  
Ulf Ottosson ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Species ◽  
Species Delimitation ◽  
Integrative Taxonomy ◽  
West African ◽  
Northwest Africa ◽  
Sub Saharan ◽  
Plateau State ◽  
Avian Family ◽  
Relic Population

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

scholarly journals Integrative taxonomy reveals a cryptic species of the nudibranch genus Polycera (Polyceridae) in European waters

2020 ◽  
Vol 100 (5) ◽  
pp. 733-752
Author(s):  
Cecilie Gotaas Sørensen ◽  
Cessa Rauch ◽  
Marta Pola ◽  
Manuel António E. Malaquias
Keyword(s):  
Species Delimitation ◽  
Molecular Phylogenetics ◽  
Mitochondrial Gene ◽  
Haplotype Network ◽  
Integrative Taxonomy ◽  
Geographic Range ◽  
Yellow Orange ◽  
Anatomical Characters ◽  
Taxonomic Approach ◽  
Barcode Gap

AbstractThis work aimed to test whether the colour variability featured by the European nudibranch Polycera quadrilineata is consistent with the concept of a single polychromatic species or may hide multiple lineages. Samples from across the geographic range of P. quadrilineata together with representatives from worldwide species with a focus on Atlantic diversity, were gathered and studied using an integrative taxonomic approach. Morpho-anatomical characters were investigated by light and scanning electron microscopy. Bayesian molecular phylogenetics using MrBayes, the Automatic Barcode Gap Discovery species delimitation method, and haplotype network analysis using the PopArt software were employed to help delimit species using the mitochondrial gene cytochrome c oxidase subunit I (COI). The results supported the existence of a second species, here described and named Polycera norvegica sp. nov., only known from Norway where it is sympatric with P. quadrilineata. The COI uncorrected p-genetic distance between the two species was estimated at 9.6–12.4%. Polycera norvegica sp. nov. differs by exhibiting a black dotted or patchy dotted pattern occasionally with more or less defined orange/brown patches, but never black continuous or dashed stripes as in P. quadrilineata. The two species share a common colouration with a whitish base and yellow/orange tubercles. Anatomically, P. norvegica sp. nov. has a weaker labial cuticle, a smaller radula with fewer rows, and only four marginal teeth, a reproductive system with a single lobed bursa copulatrix, shorter reproductive ducts, and a penis armed with two kinds of spines: needle-like and hook-shaped penile spines.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

scholarly journals Integrative taxonomy of Acrapex stem borers (Lepidoptera : Noctuidae : Apameini): combining morphology and Poisson Tree Process analyses

2014 ◽  
Vol 28 (5) ◽  
pp. 451 ◽  
Author(s):  
Bruno P. Le Ru ◽  
Claire Capdevielle-Dulac ◽  
Emmanuel F. A. Toussaint ◽  
Desmond Conlong ◽  
Johnnie Van den Berg ◽  
...  
Keyword(s):  
Molecular Species ◽  
Species Delimitation ◽  
Host Plants ◽  
Molecular Phylogenetics ◽  
Integrative Taxonomy ◽  
Imperata Cylindrica ◽  
Eastern Africa ◽  
Similar Species ◽  
Stem Borers ◽  
Lepidoptera Noctuidae

Ten morphologically similar species of Acrapex from eastern and south-eastern Africa belonging to the A. stygiata and A. albivena groups are reviewed. Six species are described as new: A. brunneella, A. mitiwa, A. mpika, A. salmona, A. sporobola and A. yakoba. The Poaceae host plants of eight species are recorded; four species, A. mitiwa. A. subalbissima, A. syscia and A. yakoba, were found developing exclusively on Imperata cylindrica (L.) Beauv., (Andropogoneae); two species, A. sporobola and A. salmona, on I. cylindrica and Sporobolus macranthelus Chiov. (Zoysieae); and A. albivena on I. cylindrica, Miscanthus capensis (Nees) Andersson (Andropogoneae) and Cymbopogon sp. (Andropogoneae). Acrapex stygiata larvae developed on M. capensis and Cymbopogon sp. The host plants of A. brunneella and A. mpika remain unknown. We also conducted molecular phylogenetics and molecular species delimitation analyses on a comprehensive sample of 49 specimens belonging to nine of the studied species. Molecular phylogenetics and molecular species delimitation analyses provided additional evidence of the validity of the six newly described species but also suggested a level of hidden biodiversity for one of them.

scholarly journals Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora)

2018 ◽  
Vol 285 (1871) ◽  
pp. 20172159 ◽  
Author(s):  
Yan Zhao ◽  
Zhenzhen Yi ◽  
Alan Warren ◽  
Weibo B. Song
Keyword(s):  
Species Delimitation ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Integrative Taxonomy ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Gene Markers ◽  
Morphological Differences ◽  
Large Subunit Rdna

Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes ( sensu lato ) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes ( sensu stricto ), Euplotoides , Euplotopsis and Moneuplotes are not supported; the vannus -type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1–D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes .

Integrative taxonomy and geographic sampling underlie successful species delimitation

The Auk ◽  
2021 ◽  
Author(s):  
Carla Cicero ◽  
Nicholas A Mason ◽  
Rosa Alicia Jiménez ◽  
Daniel R Wait ◽  
Cynthia Y Wang-Claypool ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Population Level ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Level Variation ◽  
Multiple Traits ◽  
Guiding Principle ◽  
Environmental Space ◽  
Exciting Time ◽  
Access To Data

Abstract Species delimitation requires a broad assessment of population-level variation using multiple lines of evidence, a process known as integrative taxonomy. More specifically, studies of species limits must address underlying questions of what limits the distribution of populations, how traits vary in association with different environments, and whether the observed trait differences may lead to speciation through reproductive isolation. While genomic data have revolutionized the process of delimiting species, such data should be analyzed along with phenotypic, behavioral, and ecological traits that shape individuals across geographic and environmental space. The integration of multiple traits promotes taxonomic stability and should be a major guiding principle for species delimitation. Equally important, however, is thorough geographic sampling to adequately represent population-level variation—both in allopatry and across putative contact zones. We discuss the importance of both of these factors in the context of species concepts and traits and present different examples from birds that illustrate criteria for species delimitation. In addition, we review a decade of proposals for species-level taxonomic revisions considered by the American Ornithological Society’s North American Classification Committee, and summarize the basis for decisions on whether to split or lump species. Finally, we present recommendations and discuss challenges (specifically permits, time, and funding) for species delimitation studies. This is an exciting time to be studying species delimitation in birds: many species-level questions remain, and methodological advances along with increased access to data enable new approaches to studying age-old problems in avian taxonomy.

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