The overrated use of the morphological cryptic species concept: An example with Nyctelia darkbeetles (Coleoptera: Tenebrionidae) using geometric morphometrics

Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini)

To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

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.

DNA Barcoding versus Morphological Variability of Pterostichus brevicornis brevicornis (Kirby, 1837) (Coleoptera, Carabidae) in the Arctic and Subarctic

Simple Summary

Taxonomic studies on a polymorphic species inhabiting a region with relatively uniform environmental conditions (e.g., the Arctic) should involve an integrative approach. Ground beetles such as the subgenus Cryobius of the genus Pterostichus are a successful group in expansion in the tundra biome. The current taxonomy of Cryobius species is unclear and could be considered an obstacle to ecological studies; knowledge of their distribution patterns in the Arctic is rather limited. In this study, the first report on the phylogeography and phylogeny of the most abundant tundra subspecies, P. (Cryobius) brevicornis brevicornis (Kirby, 1837), within its continuous range throughout northern Eurasia and North America is presented. The results indicated that the male genitalia morphology of P. b. brevicornis from Eurasian populations shared a higher geographic variability compared with the pronotum shape and the mitochondrial DNA sequences.

Abstract

The geographic patterns of genetic and morphological variability in ground beetles were examined throughout Northern Eurasia and North America using the most abundant circumpolar tundra subspecies, Pterostichus (Cryobius) brevicornis brevicornis (Kirby, 1837), as a model. Phylogenetic structure was assessed on the basis of a Bayesian approach using two DNA markers (partial sequences of the COI and 28S rRNA genes), while phylogeographic patterns and population genetic diversity were estimated using the COI gene only. Morphological patterns were analysed using elliptical Fourier coefficients that were calculated based on the pronotum and male genitalia shape outlines. The subspecies shares 23 COI haplotypes throughout its entire circumpolar range, while eight haplotypes of 28S rRNA were detected in Northern Eurasia. Phylogenetic analysis did not reveal subdivided species lineages with strict geographical imprint. The network, F_ST and uncorrected pairwise divergence analyses showed that the genetic distances between populations increase by longitude from Northeastern Asia to Europe. The genetic variability among the five studied geographical population groups of P. b. brevicornis was relatively high. The MANOVA showed significant regional divergence between local populations in Northern Eurasia based on both morphological markers, but only male genitalia variability was geographically structured. Neither the pronotum shape nor the male genitalia shape aligned with the phylogeographic patterns discovered on the basis of COI sequences. The genetic (COI) marker had more variation within, rather than among, population groups in addition to morphology of pronotum but not male genitalia.

The Unequal Taxonomic Signal of Mosquito Wing Cells

Simple Summary

Mosquitoes of the genus Aedes include important vectors of human disease viruses, including dengue, chikungunya and Zika. Surveillance programs used to detect and control these pests need accurate, fast and low-cost techniques to track the primary target and monitor possible re-infestations. Geometric morphometrics of mosquito wings is a convenient tool in mosquito species identification, but this method requires a complete wing in good condition for maximum accuracy. In this study, we investigate the amount of taxonomic signal provided by shape analysis of the internal cells of the wing. We show that (i) the internal cells of the wing provide differing amounts of taxonomic information, and (ii) the taxonomic signal of a given cell depends on the species under comparison. Since some of these cells are very informative, our study suggests that even damaged wings may provide key taxonomic information to differentiate among species found in mixed species surveillance collections.

Abstract

Accurate identification of mosquito species is critically important for monitoring and controlling the impact of human diseases they transmit. Here, we investigate four mosquito species: Aedes aegypti, Ae. albopictus, Ae. scutellaris and Verrallina dux that co-occur in tropical and subtropical regions, and whose morphological similarity challenges their accurate identification, a crucial requirement in entomological surveillance programs. Previous publications reveal a clear taxonomic signal embedded in wing cell landmark configuration, as well as in the external contour of the wings. We explored this signal for internal cells of the wings as well, to determine whether internal cells could uniformly provide the same taxonomic information. For each cell to be tentatively assigned to its respective species, i.e., to measure the amount of its taxonomic information, we used the shape of its contour, rather than its size. We show that (i) the taxonomic signal of wing shape is not uniformly spread among internal cells of the wing, and (ii) the amount of taxonomic information of a given cell depends on the species under comparison. This unequal taxonomic signal of internal cells is not related to size, nor to apparent shape complexity. The strong taxonomic signal of some cells ensures that even partly damaged wings can be used to improve species recognition.

Addressing the Linnean shortfall in a cryptic species complex

Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.

Measuring the Inter and Intraspecific Sexual Shape Dimorphism and Body Shape Variation in Generalist Ground Beetles in Russia

Ground beetles in multiple species vary greatly in the expression of the shape on sexual traits, resulting in a sexual shape dimorphism as a consequence of sexual selection differences. The present research focuses on the study of inter and intrasexual sexual shape dimorphism of two generalist genera of ground beetles Pterostichus and Carabus. Geometric morphometric methods were applied to five generalist species of ground beetles Carabus exaratus, C. granulatus, Pterostichus melanarius, P. niger, and P. oblongopunctatus and several multivariate analyses were applied for two different traits, abdomen and elytra. Three of the five species analyzed showed high levels of sex-based shape dimorphism. However, the most generalist species, P. melanarius and P. oblongopunctatus, did not evidence shape-based sexual dimorphism differentiation in both of the analyzed traits, as statistically confirmed based on the permutation of pairwise comparison of the Mahalanobis distances of a sex–species classifier. It is generally known that environmental stress in natural populations can affect the fitness expression, principally related to sexual fecundity, being that this pattern is more evident in non-generalist species. In our results, the contrary pattern was found, with the absence of sexual shape dimorphism for two of the three generalist species analyzed. On the other hand, the interspecies shape variation was clearly identified using principal component analysis of both of the analyzed traits. Finally, this research is the first to analyze the relationship between sexual shape dimorphism in Russian ground beetles, evidencing the lack of understanding of the mechanism underlying the sexual dimorphism, especially in species living in extreme environments.

Quantifying the Geometric Shell Shape between Populations of True Limpets Lottia Mesoleuca (Mollusca: Lottidae) in Colombia

The increasing activity in morphological studies has provided new tools to analyses the shape quantitatively, these quantitative measurements allow the researcher to examine the variation in shape and perform analysis to examine the quantitative differences among the species shapes, where geometric morphometrics has rendered great results in the last years. This study was focused on assessing the morphometric variation between populations of Lottia mesoleuca of the family Lottidae, an abundant group of gastropods in the rocky ecosystems of Bahía Málaga and Isla Gorgona (Colombian Pacific). This family has a high morphological diversity, making the identification of some morphotypes problematic work. Geometric morphometrics methods were applied on the shell using dorsal, lateral and ventral views. Different multivariate analyses were performed to differentiate the groups of species and populations (principal component analysis, morphological distances comparisons and grouping analysis by means of the Ward method). The results indicate that individuals of the species Lottia mesoleuca have key geometric characteristics associated to the different populations (depth intertidal zones) for classification, being the geometric shape of the shell enough to determine morphotypes between the different populations studied. Aspects associated with the combination of ecological variables with morphometric ones are necessary to be able to visualize with a higher resolution the structural complexity of populations and their adaptation processes. Furthermore, it is obvious that there is a strong need to conduct more explorations of environmental and ecological processes that provide some insight on why the morphological characteristics are so variable in the same species.

Molecular and morphometric identification of pistachio psyllids with niche modeling of Agonoscena pistaciae (Hemiptera: Aphalaridae)

Species of Agonoscena (Hemiptera: Aphalaridae) are key pests of pistachio in all of the most important pistachio producing countries in the Old World. The efficiency and accuracy of DNA barcoding for the identification of Agonoscena species were tested using mitochondrial cytochrome c oxidase subunit 1 (mtCO1) and cytochrome b (cytb) gene sequences. Moreover, morphometric sexual dimorphism was studied. Finally, the potential geographical distribution of Agonoscena pistaciae, the most important pistachio pest, was calculated using the MaxEnt model. Similar relationships of clustering were found in the morphometric analysis and the molecular analyses with mtCO1 and cytb genes, with A. bimaculata and A. pistaciae being closely related, and A. pegani constituting their sister group. Although the results showed that the cytb gene is a better marker for barcoding in this group, the mtCO1 gene clearly separates the three psyllid species making mtCO1 suitable for diagnostic purposes. A geometric morphometric analysis showed that the distance between landmark number 7 (bifurcation of vein M) to the fore margin of the forewing, and the distance between landmarks number 6 (apex of vein Cu1b) and 11 (wing base), are the most important geometric characters for diagnosing the studied species. Moreover, the forewing shape of males vs females is similar in A. pistaciae and A. bimaculata but differs significantly in A. pegani. In the ecological niche modeling of the distribution of A. pistaciae, the most important contribution was made by the variable 'minimum temperature of coldest period'. The most suitable areas for A. pistaciae are restricted to Eastern, Southern and some parts of Central Iran.

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.

Identification, sexual dimorphism, and allometric effects of three psyllid species of the genus Psyllopsis by geometric morphometric analysis (Hemiptera, Liviidae)

Jumping plant lice (Hemiptera: Psylloidea) are considered important vectors of plant diseases and also economically important pests in agriculture and forest ecosystems. Three psyllid species Psyllopsisrepens Loginova, 1963, Psyllopsissecuricola Loginova, 1963, and Psyllopsismachinosus Loginova, 1963 associated with the ash tree Fraxinus are morphologically very similar. So far, their distinction has been possible only by comparing their male and female genitalia. In this research, forewing shape and size characteristics, sexual dimorphism and their allometric effects, using geometric morphometric analysis, were examined for identification purposes. The results showed significant differences in wing shape and size between the species studied. Based on the results, two species P. machinosus and P.securicola can be differentiated with the vein M1+2, as in P.securicola the vein M1+2 is located between Rs and M3+4 veins, but the vein M1+2 is closer to the vein M3+4 in P.machinosus; also, P.repens can be differentiated from the two species P.machinosus and P.securicola by vein M. Hence, the veins M1+2, M3+4, Rs and M were the most important wing characters for discrimination of the three species, especially in the field. The analysis also showed significant differences in wing shape and size between male and female of the three species, and the allometric analysis showed that significant shape differences still remain in constant size in P. machinosus and P.repens. Geometric changes in the forewings of both sexes for the three species are illustrated.

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.

The wing venation patterns to identify single tsetse flies

This is the first study to explore the potential of various geometric morphometrics methods to help the morphological diagnostic of tsetse species, vectors of human and animal trypanosomiases in sub-Saharan Africa. We compared landmarks, semilandmarks and outlines techniques on male and female samples of species, and suggested adapted strategies according to the countries and their own Glossina fauna. We could compare up to 7 taxa belonging to the three main subgenera of the Glossina genus: Nemorhina (5 species), Glossina (1 species) and Austenina (1 species). Our sample included the major vectors of sleeping sickness: G. palpalis palpalis, G. p. gambiensis, G. fuscipes fuscipes and G. f. quanzensis, as well as two important vectors of African animal trypanosomoses: G. tachinoides and Glossina morsitans submorsitans. The average level of correct species recognition by the wing shape was satisfactory, and slightly higher for females than for males. The best scores of correct assignment, in both sexes, were obtained by the contour technique (96% of correct attribution in females, 92% in males), slightly higher than for semilandmarks (95% and 91%) or landmarks (94% and 89%) techniques. We made our images of wings freely available to be used as reference images (http://mome-clic.com), and we describe the conditions and the analytical steps to be followed to identify unknown specimens using external reference images. Under adequate conditions, such use of reference images obtained from a free access server could help species identification of new samples anywhere in Africa.

A taxonomy review of Oreoderus Burmeister, 1842 from China with a geometric morphometric evaluation (Coleoptera, Scarabaeidae, Valgini)

The species of the genus Oreoderus are morphologically similar, and can be challenging to distinguish without dissecting the male genitalia. In this study, the Oreoderus species from China are reviewed. Three new species of Oreoderus are described: Oreoderus dasystibialis Li & Yang, sp. n., Oreoderus brevitarsus Li & Yang, sp. n. and Oreoderus oblongus Li & Yang, sp. n. A key of the male Oreoderus and a distribution map are provided. Oreoderus coomani Paulian, 1961 was found as a new record in China. The first description of the female of Oreoderus arrowi Ricchiardi, 2001 is provided. Oreoderus humeralis Gestro, 1891, Oreoderus quadricarinatus Arrow, 1944, Oreoderus crassipes Arrow, 1944, and Oreoderus momeitensis Arrow, 1910 are excluded from the Chinese fauna. Furthermore, we utilize geometric morphometric approaches (GM) to analyze the shape variation of four characters (pronotum, elytra, protibia and aedeagus) in Oreoderus. The morphological variations of Oreoderus and the taxonomic value of each character are discussed. The combined analysis of geometric morphometrics and comparative morphology support recognition of the three new species.

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.