Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa

Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty

The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.

Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus

The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.

Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude

DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8-20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.

Similar Ones Are Not Related and Vice Versa—New Dendronotus Taxa (Nudibranchia: Dendronotidae) from the North Atlantic Ocean Provide a Platform for Discussion of Global Marine Biodiversity Patterns

One new species of the genus Dendronotus (Nudibranchia: Dendronotidae) is described from Norway and Northern Ireland, as well as from the adjacent North Sea, and one new subspecies of Dendronotus arcticus is described from Norway by applying a combination of fine-scale morphological and molecular phylogenetic data. The present case demonstrates multilevel morphological and molecular similarities and differences considering on the one hand a grouping of three similar looking sympatric taxa (D. yrjargul, D. arcticus gartensis n. subsp. and D. keatleyae n. sp.), and on the other hand two different looking apparently allopatric subspecies (D. arcticus arcticus and D. arcticus gartensis n. subsp.). The type species of the genus, D. frondosus, which is the commonest dendronotid in Norway and the United Kingdom, consistently demonstrates substantial molecular and fine-scale morphological differences from D. keatleyae n. sp. The present study, apart from providing purely taxonomic information, also provides new data for a broad discussion of global biodiversity patterns.

Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny

Ostracod shells are used extensively in paleontology, but we know little about their evolution, especially in ancient lakes. Lake Baikal (LB) is the world's most important stronghold of Candonidae diversity. These crustaceans radiated here rapidly (12-5 Ma) and with an unprecedented morphological diversity. We reconstruct their molecular phylogeny with 46 species and two markers (18S and 16S rRNA), and use it to estimate the evolution of the shell shape and size with landmark-based geometric morphometrics (LBGM). High posterior probabilities support four major clades, which differ in node depth and morphospace clustering. After removing a significant allometry, the first three principal components (PCs) describe about 88% of total variability, suggesting a strong integration. Reconstructed ancestral shapes are similar for all four clades, indicating that diversification happened after colonization. Major evolutionary changes occurred from trapezoidal to elongated shapes. Sister species are separated in morphospace, by centroid size, or both, as well as by vertical and horizontal distributions in LB. Ostracod shell is a strongly integrated structure that exhibits high evolvability, with some extreme shapes, although mostly along the first PC. This is the first study that combines molecular phylogeny and LBGM for ostracods and for any LB group.

Two New Uromunna Species (Isopoda: Asellota: Munnidae) from the Korean Peninsula and Their Phylogenetic Position within Munnoid Groups

Two new Uromunna species, Uromunna mundongensis sp. n. and Uromunna jejuensis sp. n., are described from the Korean Peninsula, representing the first record of the genus in Korean waters. Genetic analyses using two mitochondrial (COI, Cytb) and one ribosomal (18S rRNA) gene allowed us to confirm high pair-wise interspecific differences with the establishment of reliable barcoding gaps of COI (19.9%) and 18S (0.4%) between the new species. Finally, the phylogenetic relationship between the Uromunna species as well as the position of the genus within the munnoid groups are reconstructed using 18S.

Fleas from the Silk Road in Central Asia: identification of Ctenocephalides canis and Ctenocephalides orientis on owned dogs in Uzbekistan using molecular identification and geometric morphometrics

Background

The Silk Road connected the East and West for over 1500 years. Countries in Central Asia are valuable in addressing the hypothesis that parasites on domestic animals were introduced along the Silk Road. Adult fleas are obligate parasites, having worldwide distribution. In dogs, Ctenocephalides canis, C. felis and C. orientis are the most common species identified. The distribution of the Oriental cat flea, C. orientis, is restricted to southeast Asia. The purpose of this study was to determine the diversity of dog fleas from Uzbekistan, a country in Central Asia, with particular reference to C. orientis.

Methods

Fleas were collected from 77 dogs from 5 locations in Uzbekistan. The cox1 gene sequences from Ctenocephalides spp. were compared to global collection of Ctenocephalides cox1 haplotypes. Landmark-based geometric morphometrics have been applied to the head and curvature to compare C. canis and C. canis using canonical variate analysis and discriminant function analysis.

Results

Overall, 199 fleas were collected and identified as C. canis (n = 115, 58%), C. orientis (n = 53, 27%) and Pulex irritans (n = 22, 11%). None of the fleas were C. felis. All Ctenocephalides spp. fleas were subject to cox1 amplification and 95% (166/175) yielded DNA sequence. There were 25 cox1 haplotypes; 14 (22/25, 88%) were C. canis cox1 haplotypes and 3 (3/25, 12%) were C. orientis cox1 haplotypes. Molecular analysis confirmed the absence of C. felis. Four (4/22) and one (1/3) cox1 haplotypes were identical to cox1 haplotypes belonging to C. canis and C. orientis cox1 haplotypes identified elsewhere, respectively. Overall morphometric analysis confirmed significant differences between the head shape of C. canis and C. orientis and improved four–fivefold the species identification compared to traditional morphological key.

Conclusion

We report for the first time the presence of C. orientis in Uzbekistan. Differentiation of C. orientis from C. canis and C. felis remains difficult in regions where these species coexist. Studies in Central and Southeast Asia should confirm species identity using cox1 locus to enable retracing of the distribution of the Ctenocephalides in Asia. The presence of C. orientis suggests that this species may have been introduced from the east along the ancient Silk Road.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05477-3.

Deciphering “cryptic” nature of European rock-dwelling Pyramidula snails (Gastropoda: Stylommatophora)

Many molecular phylogenetic studies conclude by reporting discoveries of new “cryptic” species. However, these putative biological entities are typically left unverified outside of the dna evidence or subjected to only superficial post-hoc analyses. Minute land snails of the Western Palearctic Pyramidula represent one of such examples being considered a cryptic species complex based on previously conducted molecular phylogeny. Several species appear indistinguishable due to noticeable shell tendency towards either high-spired (Pyramidula rupestris and P. jaenensis) or low-spired (P. saxatilis and P. pusilla) morphotype. Here, we challenge this conclusion by using mt DNA, n DNA, morphometric analyses and qualitative shell features, and seek for a potential evolutionary mechanism behind the conchological similarities. Through an empirical integration of multiple data types we document that the studied taxa can be visually distinguished. Unlike isolated shell measurements, cva s based on traditional morphometrics and geometric morphometrics have power to separate all species from each other, except for P. saxatilis and P. pusilla. However, only a use of previously overlooked shell surface microsculpture makes it possible to identify individuals of all species. Considering tight associations between shell measurements and climate, we propose an evolutionary explanation based on optimization of thermal flux under different climatic selection pressures. Our study brings the awareness towards microscopic shell features, and outlines a general protocol to identify robust visual identification criteria in taxonomic groups containing cryptic (and non-cryptic) members. It also exemplifies an integration of various data types for macroscale species identification, which we believe should follow any discovery of putatively cryptic species.

Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes

Groundwater is one of our most important resources, however groundwater ecosystems are among the most understudied habitats of the planet earth. Studies on groundwater organisms are hampered by the difficult accessibility of species, the lack of morphological differentiation and the limitation for laboratory cultures. One important approach to overcome these shortcomings is to provide sensitive genetic methods to unravel patterns of biodiversity, population structure and gene flow in natural populations. In this study we present five sets of microsatellite markers developed for the isopods Asellus aquaticus and Proasellus slavus, the cyclopoides Paracyclops fimbriatus and Acanthocyclops sensitivus and the harpacticoide Bryocamptus echinatus (Crustacea). Two of these species were subjected to detailed population genetic analyses: We studied 501 specimens of Asellus aquaticus from four different regions in Northern Germany using nine microsatellite markers and 70 specimens of Bryocamptus echinatus using nine microsatellite markers from three different sampling sites in South-Western Germany. Our results show that genetic diversity is high (A. aquaticus: 10 to 20 and B. echinatus: 4 to 18 alleles per locus) among populations of aquatic invertebrates, populations are highly differentiated (F_ST > 0.2) and genetic differentiation was associated with geographic patterns. Applications of molecular genetic methods and their use for the detection of hydrological exchange processes relevant for drinking water suppliers are demonstrated and discussed.

A Hotspot of Arid Zone Subterranean Biodiversity: The Robe Valley in Western Australia

Knowledge of subterranean fauna has mostly been derived from caves and streambeds, which are relatively easily accessed. In contrast, subterranean fauna inhabiting regional groundwater aquifers or the vadose zone (between surface soil layers and the watertable) is difficult to sample. Here we provide species lists for a globally significant subterranean fauna hotspot in the Robe Valley of the Pilbara region, Western Australia. This fauna was collected from up to 50 m below ground level using mining exploration drill holes and monitoring wells. Altogether, 123 subterranean species were collected over a distance of 17 km, comprising 65 troglofauna and 58 stygofauna species. Of these, 61 species were troglobionts and 48 stygobionts. The troglofauna occurs in small voids and fissures in mesas comprised mostly of an iron ore formation, while the stygofauna occurs in the alluvium of a river floodplain. The richness of the Robe Valley is not a localized aberration, but rather reflects the richness of the arid Pilbara region. While legislation in Western Australia has recognized the importance of subterranean fauna, mining is occurring in the Robe Valley hotspot with conditions of environmental approval that are designed to ensure species persistence.

Population genetics and geometric morphometrics of the freshwater snail Segmentina nitida reveal cryptic sympatric species of conservation value in Europe

Segmentina nitida Müller 1774 is a rare European freshwater snail of drainage ditches and marshland, which has seen a marked decrease in range (~ 80%) over the last 100 years in the UK. This has been attributed to over-dredging of drainage ditches for land management, conversion of grazing marshes to arable farmland, as well as eutrophication. Segmentina nitida is identified as a priority species in the UK Biodiversity Action Plan (UKBAP) that recommends further research to inform reintroduction and translocation for its conservation. We used nuclear markers (microsatellites and ITS2) and a mitochondrial (COI) marker to investigate population structure in S. nitida individuals sampled from Poland, Germany, Sweden, and the UK to identify differences within and between populations. Data based on 2D landmark-based geometric morphometrics of S. nitida shells was used to determine if phenotypic variation followed genetic differentiation. Two distinct genetic lineages of S. nitida were identified in ITS and COI phylogenies as well as cluster analysis of microsatellite markers, one of these lineages was present in eastern Europe (Poland, Sweden- Lineage 2), and one in western Europe (UK, Germany- Lineage 1), with lineages co-occurring in German populations. No genetic admixture was observed in German populations containing both lineages. These two lineages were also distinct in shape, with lineage 2 individuals having significantly wider shells and taller and wider apertures than those in Lineage 1. ~ 85% of shells assigned to the predicted lineage in a discriminant analysis of Procrustes shape coordinates. We infer that S. nitida includes at least one sympatric cryptic species. We discuss the implications of these findings on the conservation status of S. nitida in the UK and Europe.

Patterns of intraspecific morphological variability in soil mites reflect their dispersal ability

The ability to disperse is one of the most important factors influencing the biogeography of species and speciation processes. Highly mobile species have been shown to lack geographic population structures, whereas less mobile species show genetically strongly subdivided populations which are expected to also display at least subtle phenotypic differences. Geometric morphometric methods (GMM) were now used to analyze morphological differences between European populations of a presumed non-phoretic, little mobile mite species in comparison to a highly mobile, phoretic species. The non-phoretic species Scutacarus carinthiacus showed a phenotypic population structure, whereas the phoretic species S. acarorum displayed homogeneity. These different patterns most probably can be explained by different levels of gene flow due to different dispersal abilities of the two species. GMM proved to be a sensitive tool that is especially recommendable for the analysis of (old) museum material and/or specimens in microscopic slides, which are not suitable for molecular genetic analysis.

Application of propylene glycol in DNA-based studies of invertebrates

High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.

The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.

When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.

Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.

Integrative taxonomy reveals an even greater diversity within the speciose genus Phyllodistomum (Platyhelminthes:Trematoda:Gorgoderidae), parasitic in the urinary bladder of Middle American freshwater fishes, with descriptions of five new species

Phyllodistomum is one of the most species-rich genera of parasitic platyhelminths, with 120 species described worldwide; they infect the urinary bladder of marine and freshwater fishes. As the number of new species within the genus has increased, morphological conservatism, and the lack of reliable diagnostic traits make the separation of species a challenging task. The increase of genetic data for Phyllodistomum species has permitted the use of an integrative taxonomy approach as a framework for species discovery and delimitation. DNA sequences (28S rRNA and COI mtDNA) were obtained from individuals of Phyllodistomum sampled in 29 locations across Middle America, and used in combination with morphology, host association and geographic distribution to uncover five new congeneric species. Morphologically, the new species are relatively similar; there are no unique morphological traits to readily distinguish them. We first investigated species boundaries through phylogenetic analyses of the independent and concatenated datasets; analyses recognised five candidate species showing reciprocal monophyly and strong clade support, particularly for COI data. The interspecific 28S rRNA and COI sequence divergence among the new species from 0.4 to 18.4% and from 5.1 to 27% respectively. These results were further validated by a Bayesian species delimitation approach. The five new species are well supported by molecular data used in combination with other sources of information such as host association and geographical distribution and are described herein as Phyllodistomum romualdae sp. nov., P. virmantasi sp. nov., P. isabelae sp. nov., P. scotti sp. nov., and P. simonae sp. nov.

Four new Cyclopina (Copepoda, Cyclopinidae) from South Korea

Copepods are well studied in South Korea, with the exception of marine non-parasitic cyclopoids, and especially cyclopinids; only three species were found so far here, and only one of them is endemic. A survey of intertidal interstitial faunas from sandy beaches revealed four endemic members of the genus Cyclopina Claus, 1863, which represents the first record of the largest cyclopinid genus in South Korea. A detailed study of their morphology revealed numerous differences, including in rarely studied cuticular organs. Some of these micro-characters could easily be homologised and showed little intraspecific variability, which might prove invaluable for matching sexes and reconstructing phylogenetic relationships. Cyclopinabusanensissp. nov. is described from both sexes collected near Busan (South Coast of South Korea), and is most similar to the only congener from Japan: C.kiraensis Horomi, 1984. Cyclopinakoreanasp. nov. is described from both sexes collected near Gangneung (East Coast), and has no close relatives among currently known species. Cyclopinacurtijejusp. nov. is described from two females from Jeju (off South Coast); it is possibly closely related to C.smirnovi Herbst, 1982, but the latter is known from a single male from the Russian Far East. Cyclopinawidosp. nov. is described from both sexes from Wido (West Coast), and shows numerous reductions in segmentation and armature of appendages, most of them probably a consequence of its diminutive size. A table of 26 discrete and continuous characters commonly used in the taxonomy of this group is provided for 48 valid species and subspecies of Cyclopina.

Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees

Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

Integrative taxonomy and species delimitation of Rhipicephalus turanicus (Acari: Ixodida: Ixodidae)

Rhipicephalus turanicus ticks are widely distributed across the Palearctic and Afrotropics. These two continental populations display differences in morphological characters that raise the question of a potential species boundary. However, the taxonomic status of these morphologically divergent lineages is uncertain because R. turanicus from Cyprus and Zambia have been shown to interbreed and produce fertile hybrids. We employ integrative taxonomy that considers data from mtDNA sequences (12S and 16S rDNA), geographic distribution, traditional (qualitative) morphology, as well as shape outlines of female spiracles and male adanal plates measured in a geometric morphometric framework (quantitative morphology) to resolve this taxonomic issue. Molecular lines of evidence (12S and 16S rDNA) support taxonomic separation between ticks sampled in the Afrotropics and the Palearctic. This is corroborated by qualitative and quantitative morphology. Within the Palearctic, two sub-lineages were recovered based on sequence data that loosely correspond to southern Europe and the Middle East/Asia. One new species, Rhipicephalus afranicus n. sp. is described from South Africa with a geographic distribution that extends into eastern Africa. This leaves R. turanicus sensu lato comprised of two lineages located in southern Europe and the Middle East/Asia. The type locality for R. turanicus is in Uzbekistan, thus the Middle East/Asia lineage is considered R. turanicus sensu stricto. Detailed descriptions are provided for R. afranicus n. sp. and R. turanicus sensu stricto together with high resolution images. Speciation is attributed to recent Sahara desert expansion that formed a natural barrier to dispersal approximately 5-7 million years ago. However, reproductive potential between these two species suggests that divergence time and mode of speciation were not sufficient for the development of reproductive isolation. We suggest speciation was complicated by divergence and population reintegration events driven by oscillating climatic conditions contributing to reticulate evolution and maintenance of compatibility between reproductive mechanisms. This study represents an integrative (iterative) approach to delimiting Rhipicephalus spp., and provides the first application of shape outlines for female spiracles and male adanal plates measured in a geometric morphometric framework, applied to testing species boundaries between ticks.

Assessing species boundaries in the open sea: an integrative taxonomic approach to the pteropod genus Diacavolinia

To track changes in pelagic biodiversity in response to climate change, it is essential to accurately define species boundaries. Shelled pteropods are a group of holoplanktonic gastropods that have been proposed as bio-indicators because of their vulnerability to ocean acidification. A particularly suitable, yet challenging group for integrative taxonomy is the pteropod genus Diacavolinia, which has a circumglobal distribution and is the most species-rich pteropod genus, with 24 described species. We assessed species boundaries in this genus, with inferences based on geometric morphometric analyses of shell-shape variation, genetic (cytochrome c oxidase subunit I, 28S rDNA sequences) and geographic data. We found support for a total of 13 species worldwide, with observations of 706 museum and 263 freshly collected specimens across a global collection of material, including holo‐ and paratype specimens for 14 species. In the Atlantic Ocean, two species are well supported, in contrast to the eight currently described, and in the Indo‐Pacific we found a maximum of 11 species, partially merging 13 of the described species. Distributions of these revised species are congruent with well-known biogeographic provinces. Combining varied datasets in an integrative framework may be suitable for many diverse taxa and is an important first step to predicting species-specific responses to global change.

Shedding light on the hidden world of subterranean fauna: A transdisciplinary research approach

Subterranean environments contain a diverse and unique obligate fauna: either aquatic living in the groundwater or terrestrial living in voids above the water table. In the arid region of the western part of the Australian continent, a particularly rich subterranean fauna coincides with a concentration of natural resource extraction operations. Since the inclusion of subterranean fauna in assessments of environmental impact in the mid-1990s, taxonomic research in Australia on this group of mainly invertebrates has grown exponentially. However, remaining knowledge gaps continue to frustrate both environmental regulators and development proponents due to high uncertainty in the decision-making process. In early 2017, the Western Australian Biodiversity Science Institute was tasked with leading the development of a research program to improve on the current state of knowledge of subterranean fauna. To balance the diverse environmental, economic and social needs of a range of stakeholders, transdisciplinary principles were applied to program development. A clear consensus on five broad focus areas to progress include: (1) data consolidation; (2) resilience to disturbance; (3) survey and sampling protocols; (4) abiotic and biotic habitat requirements; and (5) species delineation. In the context of these focus areas; we describe the research program development, reviewing the status of knowledge within each focus area, and the research initiatives to close the gaps in knowledge. We argue that, by adopting a transdisciplinary approach, the likelihood of success of the research program, as measured by the effective translation and adoption of research findings, will be maximized. This review is timely given the ever-increasing demand on groundwater systems for water extraction worldwide. A holistic understanding of the influence of anthropogenic activities on these ecosystems, and the functional role of organisms within them, will help to ensure that their health is not compromised.

Multilevel fine-scale diversity challenges the 'cryptic species' concept

‘Cryptic’ species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a ‘cryptic’ species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named ‘cryptic’, ‘pseudocryptic’ or ‘non-cryptic’. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a ‘cryptic’ species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the ‘cryptic’ addition to ‘species’ redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based ‘cryptic’ species into morphologically-defined ‘pseudocryptic’ ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.

Taming extreme morphological variability through coupling of molecular phylogeny and quantitative phenotype analysis as a new avenue for taxonomy

Identification of animals is often hindered by decoupling of phenotypic and molecular evolutionary rates. The Acanthocyclops vernalis (Fischer, 1853) complex is arguably the most problematic group of cyclopoids and possibly of all copepods, with diversity estimates based on morphology ranging from 2 to 34 taxa. We reconstructed their phylogeny based on one nuclear and three mitochondrial markers, revealing only four species in the Holarctic and always the following sister-species pairs: vernalis–europensis sp. nov. and robustus–americanus. Landmarks for quantitative shape analyses were collected from 147 specimens on five structures commonly used to delineate cyclopoids. Procrustes ANOVA showed small directional asymmetry in all datasets, but large sexual dimorphism in shape and size. Allometry was also highly significant. Principal component analyses of size-corrected data almost completely separated species in morphospace based on the last exopodal and endopodal segments of the fourth leg. These two structures showed the highest amount of covariation, while modularity could not be proven and a phylogenetic signal was only observed in one structure. Spinules and sensilla have a limited use in delineating species here. Calculating mean shapes and the extent of inter and intraspecific phenotypic variability opens new horizons for modern taxonomy.

DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)

DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology.

Molecular evidence for new sympatric cryptic species of Aedes albopictus (Diptera: Culicidae) in China: A new threat from Aedes albopictus subgroup?

Background

Aedes (Stegomyia) albopictus (Skuse) is an indigenous species and the predominant vector of dengue fever in China. Understanding of genetic diversity and structure of the mosquito would facilitate dengue prevention and vector control. Sympatric cryptic species have been identified in the Ae. albopictus subgroup in Southeast Asia; however, little is known about the presence and distribution of cryptic species in China. This study aimed to examine the genetic diversity, evaluate potential new cryptic sibling species, and assess the prevalence of Wolbachia infections in field populations.

Methods

Aedes adult female specimens were collected from five provinces in southern and central China during 2015–2016. Morphological identification was performed under dissection microscope. The mitochondrial DNA cytochrome c oxidase subunit 1 (cox1, DNA barcoding) locus and the ribosomal DNA internal transcribed spacer region 2 (ITS2) marker were used to examine the genetic variation, evaluate cryptic sibling species, and population structure in the field populations. Screening for the presence of Wolbachia was performed using multiplex PCR.

Results

A total of 140 individual specimens with morphological characteristics similar to Ae. albopictus were sequenced for DNA barcoding. Among these, 129 specimens (92.1%) were confirmed and identified as Ae. albopictus. The remaining 11 specimens, from 2 provinces, were identified as 2 distinct sequence groups, which were confirmed by ITS2 marker sequencing, suggesting the existence of potential cryptic species of Ae. albopictus. In Ae. albopictus, we found significant genetic differentiation and population structure between populations collected from different climate zones. Medium to high frequencies of Wolbachia infections were observed in natural Ae. albopictus populations, whereas Wolbachia was infrequent or absent in cryptic species populations.

Conclusions

Our findings highlight the population differentiation by climate zone and the presence of novel, cryptic Aedes species in China. The low prevalence of Wolbachia infections in cryptic species populations could reflect either a recent invasion of Wolbachia in Ae. albopictus or different host immune responses to this symbiont in the cryptic species. The study provides useful information for vector control and host-symbiont coevolution. Further study is needed to investigate the potential for arbovirus infection and disease transmission in the emerged cryptic species.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2814-8) contains supplementary material, which is available to authorized users.

Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

Instant taxonomy: choosing adequate characters for species delimitation and description through congruence between molecular data and quantitative shape analysis

The lack of university funding is one of the major impediments to taxonomy, partly because traditional taxonomic training takes longer than a PhD course. Understanding ranges of phenotypic variability for different morphological structures, and their use as characters for delimitation and description of taxa, is a tedious task. We argue that the advent of molecular barcoding and quantitative shape analysis makes it unnecessary. As an example, we tackle a problematic species-complex of marine copepods from Korea and Japan, approaching it as a starting taxonomist might. Samples were collected from 14 locations and the mitochondrial COI gene was sequenced from 42 specimens. Our phylogenetic analyses reveal four distinct clades in Korea and Japan, and an additional nine belonging to a closely related complex from other parts of the Northern Pacific. Twenty different morphological structures were analysed for one Japanese and two Korean clades using landmark-based two-dimensional geometric morphometrics. Although there is no single morphological character that can distinguish with absolute certainty all three cryptic species, most show statistically significant interspecific differences in shape and size. We use five characters to describe two new species from Korea and to re-describe Tigriopus japonicus Mori, 1938 from near its type locality.

Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach

The number of subterranean taxa discovered in the north of Western Australia has substantially increased due to the requirements for environmental surveys related to mining development. Challenges in estimating subterranean biodiversity and distributions are related to lack of knowledge of taxa with convergent morphological characters in a largely unobservable ecosystem setting. An integrated approach is warranted to understand such complexity. Bathynellidae occur in most Australian aquifers, but only one species has been described so far, and the group lacks a reliable taxonomic framework. A new genus and one new species from the Pilbara region of Western Australia, Pilbaranella ethelensis, gen. et sp. nov., is described using both morphological and molecular data. Three additional species of Pilbaranella are defined through mitochondrial and nuclear genes, using Automatic Barcode Gap Discovery and Poisson Tree Processes species delimitation methods. A comparison of morphology and 18S rRNA sequences between Pilbaranella, gen. nov. and known lineages provides the evidentiary basis for the decision to establish a new genus. This study provides a morphological and molecular framework to work with Bathynellidae, especially in Australia where a highly diverse fauna remains still undescribed.

Systematics and diversification of Anindobothrium Marques, Brooks & Lasso, 2001 (Eucestoda: Rhinebothriidea)

Tapeworms of the genus Anindobothrium Marques, Brooks & Lasso, 2001 are found in both marine and Neotropical freshwater stingrays of the family Potamotrygonidae. The patterns of host association within the genus support the most recent hypothesis about the history of diversification of potamotrygonids, which suggests that the ancestor of freshwater lineages of the Potamotrygonidae colonized South American river systems through marine incursion events. Despite the relevance of the genus Anindobothrium to understand the history of colonization and diversification of potamotrygonids, no additional efforts were done to better investigate the phylogenetic relationship of this taxon with other lineages of cestodes since its erection. This study is a result of recent collecting efforts to sample members of the genus in marine and freshwater potamotrygonids that enabled the most extensive documentation of the fauna of Anindobothrium parasitizing species of Styracura de Carvalho, Loboda & da Silva, Potamotrygon schroederi Fernández-Yépez, P. orbignyi (Castelnau) and P. yepezi Castex & Castello from six different countries, representing the eastern Pacific Ocean, Caribbean Sea, and river basins in South America (Rio Negro, Orinoco, and Maracaibo). The newly collected material provided additional specimens for morphological studies and molecular samples for subsequent phylogenetic analyses that allowed us to address the phylogenetic position of Anindobothrium and provide molecular and morphological evidence to recognize two additional species for the genus. The taxonomic actions that followed our analyses included the proposition of a new family, Anindobothriidae fam. n., to accommodate the genus Anindobothrium in the order Rhinebothriidea Healy, Caira, Jensen, Webster & Littlewood, 2009 and the description of two new species-one from the eastern Pacific Ocean, A. carrioni sp. n., and the other from the Caribbean Sea, A. inexpectatum sp. n. In addition, we also present a redescription of the type species of the genus, A. anacolum (Brooks, 1977) Marques, Brooks & Lasso, 2001, and of A. lisae Marques, Brooks & Lasso, 2001. Finally, we discuss the paleogeographical events mostly linked with the diversification of the genus and the protocols adopted to uncover cryptic diversity in Anindobothrium.

A potential pitfall in studies of biological shape: Does size matter?

The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.

A complete survey of normal pores on a smooth shell ostracod (Crustacea): Landmark-based versus outline geometric morphometrics

Pores and sensilla on ostracod shell have often been used in studies of ontogeny, taxonomy, and phylogeny of the group. However, an analysis of sexual dimorphism and variation between valves in the number and distribution of pores is lacking. Also, such studies have never been done on a widely distributed, morphologically variable, and weakly ornamented freshwater ostracod. Here, we survey pores in one such species, Physocypria kraepelini. We choose 27 homologous pores as landmarks for 2D-geometric morphometric analysis, with the aim to assess intersexual and between valves variation in size and shape relative to the Fourier outline analysis. This species has only simple (Type A) pores with and without a lip, and each pore carries an undivided sensory seta. Our results show that the total number of pores varies (from 270 to 296), but this is not associated with a specific valve. Males carry fewer pores than females, however no sex specific pores are found. Small intrapopulation divergence of the Cyt b molecular marker (1%) indicates that morphological variability is not species related. We found that P. kraepelini exhibits directional asymmetry of size and shape, sexual size dimorphism (SSD) but lacks sexual shape dimorphism (SShD). Two geometric morphometrics methods were congruent in the estimation of SSD, SShD, and directional asymmetry of shape but differ in the statistical evaluation of directional asymmetry of size. Contrary to other animal groups, our study suggests that ostracods have more pronounced directional asymmetry of shape compared to directional asymmetry of size.

By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida)

As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila. GMYC from trees calculated using three different molecular clocks were compared, in some lineages different primary species hypotheses were returned by analyses of trees estimated under different clock models, suggesting clock model selection should be a routine component of phylogeny reconstruction for tree-based species delimitation methods, such as GMYC. Our results suggest that a minimum of 71 Plagiochilaceae species occur in Australasia, 16 more than currently accepted for the region, comprising 8 undetermined species and 8 synonyms requiring reinstatement. Despite modern taxonomic investigation over a four decade period, (1) real diversity is 29% higher than currently recognized; and (2) 12 of 33, or 36%, of currently accepted and previously untested Australasian species have circumscription issues, including polyphyly, paraphyly, internal phylogenetic structure, or combinations of two or more of these issues. These both reflect the many challenges associated with grouping decisions based solely on morphological data in morphologically simple yet polymorphic plant lineages. Our results highlight again the critical need for combined molecular-morphological datasets as a basis for resolving robust species hypotheses in species-rich bryophyte lineages.