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The genus Euhemisphaerius Chan & Yang, 1994 (Hemiptera: Fulgoromorpha: Issidae: Issinae: Hemisphaeriini) is revised. Based on a comparative morphological study and molecular phylogenetic analyses, Epyhemisphaerius Chan & Yang, 1994 and Gnezdilovius Meng, Webb & Wang, 2017 are downgraded to junior synonyms of Euhemisphaerius. This redefined genus was recovered as a well-supported clade nested within the subtribe Hemisphaeriina. Hemisphaerius delectabilis Schumacher, 1914, Gergithus flaviguttatus Hori, 1969, Ge. satsumensis Matsumura, 1916, Ge. okinawanus Matsumura, 1936 and Ge. taiwanensis Hori, 1969 are transferred to Euhemisphaerius. New synonyms are proposed: Eu. bistriatus (Schumacher, 1915), comb. nov. = Ep. rosticus (Chan & Yang, 1994), syn. nov.; Eu. delectabilis (Schumacher, 1914), comb. nov. = Gn. lineatus (Kato, 1933), syn. nov.; Eu. robustus (Schumacher, 1915), comb. nov. = Gn. robustus hoozanensis (Schumacher, 1915), syn. nov.; Eu. stramineus (Hori, 1969), comb. nov. = Ep. nummarius (Chan & Yang, 1994), syn. nov.; Eu. taiwanensis (Hori, 1969), comb. nov. = Eu. infidus Chan & Yang, 1994, syn. nov. = Eu. primulus Chan & Yang, 1994, syn. nov. Ge. rugiformis Zhang & Che, 2009, transferred to Gnezdilovius by previous authors, is considered as of uncertain generic placement and reinstated in its original combination. Gn. transversus Meng, Qin & Wang, 2020 is formally transferred to Euhemisphaerius due to the synonymy of Gnezdilovius with the latter genus, but is considered as of uncertain generic placement. Eu. paradelectabilis sp. nov. is described based on an integrative morphological, molecular and ecological approach; the new species exhibits a broad intraspecific variability in its color in a way similar to Eu. delectabilis comb. nov., but it can be readily recognized based on the lack of a shining transverse band on the frons, a character invariably present in Eu. delectabilis comb. nov. Doubtful distribution records of 11 species formerly placed into Gnezdilovius and Epyhemisphaerius are corrected and discussed.http://zoobank.org/urn:lsid:zoobank.org:pub:D5E90CE1-F4F2-48E0-B80B-3992709E4036

Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.

The ant Plagiolepis taurica Santschi, 1920 (Hymenoptera, Formicidae) is a typical species of the Eurasian steppes, a large grassland dominated biome that stretches continuously from Central Asia to Eastern Europe and is represented by disjunct outposts also in Central and Western Europe. The extent of this biome has been influenced by the Pleistocene climate, and steppes expanded recurrently during cold stages and contracted in warm stages. Consequently, stenotopic steppe species such as P. taurica repeatedly went through periods of demographic expansion and severe isolation. Here, we explore the impact of these dynamics on the genetic diversification within P. taurica. Delimitation of P. taurica from other Plagiolepis species has been unclear since its initial description, which raised questions on both its classification and its spatiotemporal diversification early on. We re‐evaluate species limits and explore underlying mechanisms driving speciation by using an integrative approach based on genomic and morphometric data. We found large intraspecific divergence within P. taurica and resolved geographically coherent western and eastern genetic groups, which likewise differed morphologically. A morphometric survey of type material showed that Plagiolepis from the western group were more similar to P. barbara pyrenaica Emery, 1921 than to P. taurica; we thus lift the former from synonymy and establish it as separate species, P. pyrenaica stat. rev. Explicit evolutionary model testing based on genomic data supported a peripatric speciation for the species pair, probably as a consequence of steppe contraction and isolation during the mid‐Pleistocene. We speculate that this scenario could be exemplary for many stenotopic steppe species, given the emphasized dynamics of Eurasian steppes. [ABSTRACT FROM AUTHOR]

Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mt genome introgression has occurred. Here, we illustrate how mt genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mt variation, and thousands of nuclear single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated 2 clades, with O. grahami and Odorrana junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support 3 species with distinct genetic clusters. These 3 distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis , as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mt genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mt introgression. [ABSTRACT FROM AUTHOR]

Water mites (Hydrachnidia) are good model organisms for the assessment and long-term monitoring of the biological impacts of natural and human-induced environmental changes in freshwater ecosystems, including those related to global climate change. However, monitoring programs using water mites as bioindicators may be impeded by difficulties associated with species identification. Here we integrate conventional morphology, DNA sequence data (using the COX1 barcoding locus) and extensive voucher photo documentation to create and validate a tool for accurate species identification of water mites in Western Siberia (including a dedicated reference climate monitoring and research site). Using this approach, we detected a total of 95 species, of which, one was a conventional new species; 14 taxa were cryptic species having large among-species COX1 K2P distances but lacking any apparent morphological differences. Our a priori species delimitation was successfully validated a posteriori. An automatic species delimitation algorithm (ASAP) identified exactly the same set of 95 species, with a species delimitation threshold of 6.1%. This result agrees with previous works suggesting a large threshold of 5.6–6.0% for water mites, but contrasts with the BOLD approach which uses a much lower threshold to identify BINs (1%). Furthermore, by comparing our identified sequences with GenBank data, we expanded known geographic ranges of several water mite species. Using extensive GenBank data on mites in Canadian waters, four species were detected to be Holarctic rather than Palaearctic as thought previously (Lebertia obscura, Limnesia undulatoides, Oxus nodigerus and Arrenurus papillator). Four species, Lebertia obscura, Torrenticola brevirostris, Hygrobates limnocrenicus and Unionicola parvipora, were recorded for the first time in Russia. We provide an annotated species checklist reporting the distribution, ecology, bioindiocation potential, and COX1 barcode sequence data along with high-resolution photographs of each DNA voucher. Future ecological and biodiversity studies will benefit from using molecular tools for accurate identification of useful mesofaunal bioindicator organisms, such as water mites. [ABSTRACT FROM AUTHOR]

Lineage‐based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage‐only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive‐mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data–ISSRseq–demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach. [ABSTRACT FROM AUTHOR]

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean‐montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome‐wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent‐based phylogenetic reconstructions, integrative Bayesian model‐based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species. [ABSTRACT FROM AUTHOR]

Accurate delimitation of species is crucial for a stable taxonomy, which provides the foundation for the study of evolutionary biology, ecology, and essentially all biological disciplines. Several approaches toward impartial and repeatable taxonomic practices are available but all existing methods have potentially unacceptable shortcomings. In particular, problems can arise when the underlying model assumptions are violated, for instance, in the presence of reduced gene flow. This is observed in the context of sex-biased dispersal, which is a common but underappreciated feature in many groups of organisms. Previously, simulations have indicated that sex-biased dispersal may lead to erroneous estimations of the true species numbers. However, this phenomenon has never been examined using empirical data. We evaluate the bias introduced by extreme female philopatry on a range of de novo [GMYC, PTP, ABGD, statistical parsimony, trinomial distribution of triplets model (tr2)] and validation (STACEY, iBPP) approaches to species delimitation in the scarab beetle genus Pachypus. Since female philopatry exhibited in this genus in particular can affect mitochondrial gene flow, we compared the results from analyses of single loci, mitochondrial loci, nuclear loci and combined data, as well as the performance of morphometric data as a secondary data source in a fully integrative Bayesian framework. Large overestimation of species numbers was observed across all analyses of combined and mitochondrial DNA data sets, suggesting specimens from nearly every sampling location as separate species. The use of nuclear data resulted in more reasonable estimations of species boundaries, which were largely supported by morphometrics of linear measurements, while geometric morphometrics of body outlines resulted in stronger splitting. Simulations of population divergence with migration, corresponding to the biology of Pachypus, showed that female philopatry strongly increases reciprocal monophyly of mitochondrial markers and may substantially contribute to over-splitting in species delimitation. Robust results recovered using nuclear DNA and morphological data nevertheless enabled us to reach novel conclusions about species boundaries in Pachypus. Our findings suggest that mitochondrial DNA will be less suited to species delimitation in many cases, in particular in the presence of sex-biased dispersal. [ABSTRACT FROM AUTHOR]

Abstract: Although resolving phylogenetic relationships and establishing species limits are primary goals of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent‐based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic‐based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters and sex‐based trait variation for developing alternative species delimitation hypotheses. The best‐supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well‐resolved lineages and the other comprising a four‐lineage polytomy and a well‐differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information content and differences between sexes in among‐taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early stages of divergence where conflicting inferences are more prone to appear. [ABSTRACT FROM AUTHOR]

Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mt genome introgression has occurred. Here, we illustrate how mt genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mt variation, and thousands of nuclear single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated 2 clades, with O. grahami and Odorrana junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support 3 species with distinct genetic clusters. These 3 distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis , as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mt genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mt introgression., Competing Interests: The authors declare no competing interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of Editorial Office, Current Zoology.)

• Multiple evidences were used to delimit species of Rhinolophus macrotis complex. • A new taxonomic treatment is proposed for the R. osgoodi. • Evolutionary processes were reconstructed following species delimitation. • Hybridization and introgression have contributed to the reticulate evolution. Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus , R. siamensis , and R. osgoodi , within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial–interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation. [ABSTRACT FROM AUTHOR]