Species delimitation using morphology, morphometrics, and molecules: definition of the Ophionscutellaris Thomson species group, with descriptions of six new species (Hymenoptera, Ichneumonidae)

Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae)

Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.

Species morphospace boundary revisited through wing phenotypic variations of Antodynerus species (Hymenoptera: Vespidae: Eumeninae) from the Indian subcontinent

The main objective of this study was to investigate the taxonomic significance of wing phenotypic variations (size and shape) for classifying potter wasps. This is the first study investigating the wing size and shape variations, as well as wing asymmetry, sexual dimorphism, wing integration, and phylogenetic signal analysis of all known Antodynerus species from the Indian subcontinent: A. flavescens, A. limbatus, and A. punctatipennis. We used forewings and hindwings for geometric morphometric analysis, and we proved that each species’ wing had unique size and shape variations, as well as significant right–left wing asymmetry and sexual dimorphism across the Antodynerus species, as verified by discriminant function analysis. Wings of Vespidae are longitudinally folded; based on that, we tested two alternative wing modular hypotheses for evaluating the wing integration, using two subsets organization, such as anterior–posterior (AP) and proximal-distal (PD) wing modular organization. We proved that Antodynerus species wings are highly integrated units (RV > 0.5), and we rejected our hypothesis at p < 0.05. The morphospace distribution analysis revealed that each species has its unique morphospace boundary, although they share some level of homoplasy, which suggests to us that we can use wing morphometric traits for Antodynerus species delimitation. In addition, we revealed the phylogenetic signal of Antodynerus species. Surprisingly, we found a shape-related phylogenetic signal in the forewing, and there is no significant (p > 0.05) phylogenetic signal in forewing size, hindwing shape, and size. We observed that the Antodynerus species’ forewing shape is evolutionarily more highly constrained than the hindwing. We found that A. limbatus and A. flavescens with distinct geographical distribution share a similar evolutionary history, while A. punctatipennis evolved independently.

Classifying fossil Darwin wasps (Hymenoptera: Ichneumonidae) with geometric morphometrics of fore wings

Linking fossil species to the extant diversity is often a difficult task, and the correct interpretation of character evidence is crucial for assessing their taxonomic placement. Here, we make use of geometric morphometrics of fore wings to help classify five fossil Darwin wasps from the Early Eocene Fur Formation in Denmark into subfamilies and often tribes. We compile a reference dataset with 342 fore wings of nine extant subfamilies and nine relevant fossil species. Since geometric morphometrics was mostly ignored in the past in Darwin wasp classification, the dataset is first used to examine differences and similarities in wing venation among subfamilies. In a next step, we used the reference dataset to inform the classification of the fossil species, which resulted in the description of one new genus and five new species, Crusopimpla weltii sp. nov., Ebriosa flava gen. et sp. nov., Entypoma? duergari sp. nov., Lathrolestes? zlatorog sp. nov., and Triclistus bibori sp. nov., in four different subfamilies. Carefully assessing data quality, we show that the fore wing venation of fossil Darwin wasps is surprisingly suitable to assign them to a subfamily or even lower taxonomic level, especially when used in conjunction with characters from other parts of the body to narrow down a candidate set of potential subfamilies and tribes. Our results not only demonstrate a fast and useful approach to inform fossil classification but provide a basis for future investigations into evolutionary changes in fore wings of ichneumonids. The high informativeness of wing venation for classification furthermore could be harvested for phylogenetic analyses, which are otherwise often hampered by homoplasy in this parasitoid wasp family.

Integrative Taxonomy of Dermacentor variabilis (Ixodida: Ixodidae) with Description of a New Species, Dermacentor similis n. sp

Dermacentor variabilis is the most widely distributed three-host tick in North America, and transmits a variety of pathogens. Within the United States, this species has a discontinuous distribution, widespread east of the Rocky Mountains and with a few populations west of the Rockies. Phylogenetic evidence based on individual markers or relatively small data sets has suggested that populations at both sides of this geographic barrier may correspond to two different species. In this study, we further explore this hypothesis using an integrative taxonomy framework. Both molecular (mitochondrial and nuclear markers) and morphological analyses of specimens collected from central-eastern and western states were performed to explore species delimitation in this taxon. Results from these analyses were consistent, and provide strong evidence that D. variabilis actually corresponds to two species. Herein, the western populations are described as a new species, Dermacentor similis n. sp. The usefulness of integrative taxonomy in the context of species delimitation is also discussed.

Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan

The predominantly tropical ophionine genus Enicospilus Stephens, 1835 is one of the largest genera of Darwin wasps (Hymenoptera, Ichneumonidae), with more than 700 extant species worldwide that are usually crepuscular or nocturnal and are parasitoids of Lepidoptera larvae. In the present study, the Japanese species of Enicospilus are revised using an integrative approach (combined morphology and DNA barcoding). On the basis of 3,110 specimens, 47 Enicospilus species are recognised in Japan, eight of which are new species (E.acutus Shimizu, sp. nov., E.kunigamiensis Shimizu, sp. nov., E.limnophilus Shimizu, sp. nov., E.matsumurai Shimizu, sp. nov., E.pseudopuncticulatus Shimizu, sp. nov., E.sharkeyi Shimizu, sp. nov., E.takakuwai Shimizu, sp. nov., and E.unctus Shimizu, sp. nov.), seven are new records from Japan (E.jilinensis Tang, 1990, E.laqueatus (Enderlein, 1921), E.multidens Chiu, 1954, stat. rev., E.puncticulatus Tang, 1990, E.stenophleps Cushman, 1937, E.vestigator (Smith, 1858), and E.zeugos Chiu, 1954, stat. rev.), 32 had already been recorded in Japan; three (E.biharensis Townes, Townes & Gupta, 1961, E.flavicaput (Morley, 1912), and E.merdarius (Gravenhorst, 1829)) have been erroneously recorded from Japan based on misidentifications, and four names that were previously on the Japanese list are deleted through synonymy. The following taxonomic changes are proposed: E.vacuus Gauld & Mitchell, 1981, syn. nov. (= E.formosensis (Uchida, 1928)); E.multidensstat. rev.; E.striatus Cameron, 1899, syn. nov. = E.lineolatus (Roman, 1913), syn. nov. = E.uniformis Chiu, 1954, syn. nov. = E.flatus Chiu, 1954, syn. nov. = E.gussakovskii Viktorov, 1957, syn. nov. = E.striolatus Townes, Townes & Gupta, 1961, syn. nov. = E.unicornis Rao & Nikam, 1969, syn. nov. = E.unicornis Rao & Nikam, 1970, syn. nov. (= E.pungens (Smith, 1874)); E.iracundus Chiu, 1954, syn. nov. (= E.sakaguchii (Matsumura & Uchida, 1926)); E.sigmatoides Chiu, 1954, syn. nov. (= E.shikokuensis (Uchida, 1928)); E.yamanakai (Uchida, 1930), syn. nov. (= E.shinkanus (Uchida, 1928)); E.ranunculus Chiu, 1954, syn. nov. (= E.yezoensis (Uchida, 1928)); and E.zeugosstat. rev. = E.henrytownesi Chao & Tang, 1991, syn. nov. In addition, the following new regional and country records are also provided: E.flavocephalus (Kirby, 1900), E.puncticulatus, and E.vestigator from the Eastern Palaearctic region, E.laqueatus from the Eastern Palaearctic and Oceanic regions, and E.maruyamanus (Uchida, 1928) from the Oriental region; E.abdominalis (Szépligeti, 1906) from Nepal, E.flavocephalus from Laos, E.formosensis from Laos and Malaysia, E.insinuator (Smith, 1860) from Taiwan, E.maruyamanus from India and Philippines, E.nigronotatus Cameron, 1903, E.riukiuensis (Matsumura & Uchida, 1926), and E.sakaguchii from Indonesia, E.pungens from 14 countries (Australia, Bhutan, Brunei, Indonesia, Laos, Malaysia, Nepal, New Caledonia, Papua New Guinea, Philippines, Solomon Islands, Sri Lanka, Tajikistan, and Taiwan), and E.yezoensis from South Korea. An identification key to all Japanese species of Enicospilus is proposed. Although 47 species are recognised in the present study, approximately 55 species could potentially be found in Japan based on ACE and Chao 1 estimators. The latitudinal diversity gradient of Enicospilus species richness is also tested in the Japanese archipelago based on the constructed robust taxonomic framework and extensive samples. Enicospilus species richness significantly increases towards the south, contrary to the ‘anomalous’ pattern of some other ichneumonid subfamilies.

New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications

Background

Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups.

Results

Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units.

Conclusions

Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy

Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses.

Eyes on the size: accuracy of visual length estimates of white sharks, Carcharodon carcharias

Visual estimates have been used extensively to determine the length of large organisms that are logistically challenging to measure. However, there has been little effort to quantify the accuracy or validity of this technique despite inaccurate size estimates leading to incorrect population assessments and misinformed management strategies. Here, we compared visually estimated total length measurements of white sharks, Carcharodon carcharias, during cage-diving operations with measurements obtained from stereo-video cameras and assessed the accuracy of those estimates in relation to suspected biases (shark size, and observer experience and gender) using generalized linear mixed-models and linear regressions. Observer experience on board cage-diving vessels had the greatest effect on the accuracy of visual length estimates, with scientists being more accurate (mean accuracy ± standard error: 23.0 ± 16.5 cm) than crew (39.9 ± 33.8 cm) and passengers (49.4 ± 38.5 cm). Observer gender and shark size had no impact on the overall accuracy of visual length estimates, but passengers overestimated sharks less than 3 m and underestimated sharks greater than 3 m. Our findings show that experience measuring animals is the most substantial driver of accurate visual length estimates regardless of the amount of exposure to the species being measured. Scientists were most accurate, even though crew observe white sharks more frequently. Our results show that visual length estimates are not impacted by shark size and are a valid measurement tool for many aspects of C. carcharias research, provided they come from people who have previously been involved in measuring animals, i.e. scientists.

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.

Towards the automated identification of Chrysomya blow flies from wing images

The Old World screwworm fly (OWSF), Chrysomya bezziana (Diptera: Calliphoridae), is an important agent of traumatic myiasis and, as such, a major human and animal health problem. In the implementation of OWSF control operations, it is important to determine the geographical origins of such disease-causing species in order to establish whether they derive from endemic or invading populations. Gross morphological and molecular studies have demonstrated the existence of two distinct lineages of this species, one African and the other Asian. Wing morphometry is known to be of substantial assistance in identifying the geographical origin of individuals because it provides diagnostic markers that complement molecular diagnostics. However, placement of the landmarks used in traditional geometric morphometric analysis can be time-consuming and subject to error caused by operator subjectivity. Here we report results of an image-based approach to geometric morphometric analysis for delivering wing-based identifications. Our results indicate that this approach can produce identifications that are practically indistinguishable from more traditional landmark-based results. In addition, we demonstrate that the direct analysis of digital wing images can be used to discriminate between three Chrysomya species of veterinary and forensic importance and between C. bezziana genders.

Forensically Relevant Blow Flies in Lebanon Survey and Identification Using Molecular Markers (Diptera: Calliphoridae)

Calliphoridae are among the first insects associated to decomposing animal remains. We have collected 1,841 specimens of three calliphorid genera: Calliphora, Lucilia, and Chrysomya, from different Lebanese localities as a first step in implementing a database of insects of forensic relevance for the country. Blow-flies are crucial for the estimation of the postmortem interval. DNA-based identification is a rapid and accurate method, often used for morphologically similar species, especially for immatures or incomplete specimens. In this study, we test the suitability of three genetic markers to identify adults and immature stages of calliphorids, viz., mitochondrial cytochrome c oxidase subunit I (COI) barcode, a region including partial sequences of mitochondrial Cyt-b-tRNAser-ND1, and second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA. Forty Lebanese specimens of various developmental stages (egg, larva, wandering third instar, pupa, newly emerged adult, and mature adult) were identified among the three calliphorid genera: Calliphora, Lucilia, and Chrysomya, and compared with published sequences to confirm their specific assignation. Phylogenetic analyses showed the robustness of ITS2 and COI to identify calliphorids at species level. Nevertheless, ITS2 failed to discriminate Lucilia caesar (Linnaeus) (Diptera, Calliphoridae) from Lucilia illustris (Meigen) (Diptera, Calliphoridae), and COI had a similar issue with Lucilia sericata (Meigen) (Diptera, Calliphoridae) and Lucilia cuprina (Wiedemann) (Diptera, Calliphoridae). Thus, these two markers are complementary. This work contributes new nucleotide sequences for Lebanon. It is a first step in implementing a molecular database of forensic relevant insects for the country.

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.

A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae)

A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented.

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

Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.

Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae)

DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.

The Mycetophilaruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data

European species of the Mycetophilaruficollis group are compared on the basis of morphology and sequences of mitochondrial cytochrome oxidase subunit one (COI) and the ITS2 region of nuclear ribosomal DNA. The study represents the first evaluation of morphology-based species delimitation of closely related fungus gnat species by applying molecular information. Detailed descriptions and illustrations of the male terminalia are presented along with a key for the identification of all nine European species of the group. Phylogenetic analyses of molecular data generally supported the morphological species discrimination. The barcoding region of COI superseded ITS2 rDNA in resolving species. In the COI barcoding region interspecific differences ranged from 2.9 to 10.6% and the intraspecific distance from 0.08 to 0.8%. Only COI data distinguished between the similar and closely related Mycetophilaichneumonea and Mycetophilauninotata of which the latter was observed to include cryptic species. The host range of some species is suggested to be narrower than previously considered and to depend on the forest type. Presented evidence indicates the importance of analysing sequence data of morphologically very similar mycetophages reared from identified host fungi for elucidating species delimitation as well as their geographic and host ranges. New country records, viz. Estonia for Mycetophilaevanida, Georgia for Mycetophilaichneumonea, Mycetophilaidonea and Mycetophilaruficollis, and Norway for Mycetophilastrobli, widen the known distribution ranges of these species.