An integrative approach to species delineation incorporating different species concepts: a case study of Limnadopsis (Branchiopoda: Spinicaudata)

New leptestherid clam shrimps (Pancrustacea: Branchiopoda: Spinicaudata: Leptestheriidae) from peninsular India

Spinicaudatan clam shrimps are an evolutionarily ancient lineage restricted to temporary freshwater pools. Use of classical morpho-taxonomic approaches alone have led to some issues in the taxonomy of this group, which are now being resolved through integrative taxonomy. Here, we describe two new leptestherid spiny clam shrimps Leptestheria chalukyae sp. nov. and Leptestheria gomantaki sp. nov. from peninsular India based on their unique morphological characters and distinct phylogenetic position. We also re-describe Leptestheria nobilis and present an overview of the morphological characters of all the Indian leptestherids. Most of the conventional taxonomic characters appear to overlap among all the Indian species, although the combination of occipital condyle shape and the cercopod marginal spines arrangement in combination, appear to be useful in separating leptestherid species.

Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean

The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions.

A taxonomic approach on diagnostic characters used to define new pterosaur taxa and an estimation of pterosaur diversity

Diagnostic characters from 227 pterosaur species were listed, separated into cranial or post-cranial elements and counted. From 21 post-cranial and 23 cranial elements, most diagnostic characters were related to phalanges (15%) and rostrum. Post-cranial characters comprise 44.23%, and cranial characters 55.77% of all characters used in pterosaur diagnoses. The highest correlation between diagnostic features occurs between the coracoid and the scapula. 25.11% and 28.63% of sampled taxa were diagnosed with 3-4 and 5-6 characters, respectively. The mean number of 6.79 characters was found in specimens with both cranial and post-cranial elements, and 4.86 and 4.17 in those with just cranial or post-cranial elements, respectively. 31 from 227 species (13.7%) were erected based on single elements, which are most frequently complete or partial mandibles (n=18). We estimate that 23.4% of the total pterosaur genera are currently known, with 90% of this diversity to be unveiled up to 2145. As the requirements of broad and cautious revision of genus/group must be undertaken, and some deposits will provide mostly fragmented and incomplete material, the assignment of fairly incomplete specimens to the most inclusive taxonomic level is feasible. Tracing this scenario can guide future works on the description of new pterosaur taxa.

Species boundaries and phylogeographic patterns in new species of Nannoniscus (Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology

Spatial patterns of genetic variation (based on COI and 16S mtDNA) for morphologically similar species in the isopod genus Nannoniscus G.O. Sars. 1870 were examined that occur broadly across the Clarion Clipperton Fracture Zone (CCZ). Samples were obtained from five different licence areas as well as an Area of Particular Environmental Interest (APEI-6) with sites located at various distances (a few to several hundred kilometres) from one another. Applying three different species delimitation (SD) methods (sGMYC, mPTP and ABGD) of the molecular data, we could distinguish between four and 12 different molecular taxonomic operational units (MOTUs). Morphological analyses could confirm five distinct phenotypic clades that represent species new to science and are described here: Nannoniscus brenkei sp. nov., Nannoniscus hilario sp. nov., Nannoniscus magdae sp. nov., Nannoniscus menoti sp. nov. and Nannoniscus pedro sp. nov. Despite the assumed limited dispersal capacity of Nannoniscus species, we found haplotypes of two species to be geographically widespread (up to > 1400 km apart), as opposed to several divergent clades occurring in close vicinity or even sympatry. Geographic distance appeared to explain the phylogeographic structure of Nannoniscus species to some extent, although oceanographic features and level of environmental heterogeneity were probably equally important.

The more the merrier: unparalleled sympatric species richness in a sea spider genus (Pycnogonida : Callipallenidae : Pallenella) from Tasmanian waters

Southern Australian waters feature remarkably diverse assemblages of the sea spider family Callipallenidae Hilton, 1942. The most speciose of the three Australian-endemic genera currently recognised has been known as Meridionale Staples, 2014, but is here reinstated under the name Pallenella Schimkewitsch, 1909 based on its type species Pallenella laevis (Hoek, 1881). This genus includes several brightly coloured forms that occur in high abundance on arborescent bryozoans. However, considerable similarity of congeners and scarcity of diagnostic characters continue to render species delineation in this genus challenging. Using an integrative taxonomic approach, we combine detailed morphological investigation with analysis of two genetic markers (mitochondrial cytochrome c oxidase subunit I, and nuclear rDNA including internal transcribed spacers 1 and 2) to explore the extraordinary species richness of the genus Pallenella in south-east Tasmania. In agreement with our morphology-based segregation of different species and morphotypes, we recovered well-supported corresponding clades in the genetic analyses. Strong mito-nuclear concordance in the two markers supports the inference of sustained reproductive isolation between the sympatrically occurring forms. Based on these findings, we distinguish a total of 13 Tasmanian congeners, representing the most diverse assemblage of sympatric species in the same microhabitat reported for a single pycnogonid genus. Within this assemblage, we (1) record the type species P. laevis for the first time after almost 150 years, (2) delineate the two Tasmanian morphotypes of the provisional ‘variabilis’ complex, and (3) describe two species new to science (P. karenae, sp. nov., P. baroni, sp. nov.). Despite considerable genetic divergences between most congeners, only few and often subtle characters are found to be suitable for morphology-based delineation. Notably, colouration of living specimens is suggested to be informative in some cases. For morphology-based species identification of preserved specimens, a key relying on combinations of characters rather than single diagnostic features is proposed.

Genetic differentiation in mountain-dwelling clam shrimp, Paralimnadia (Crustacea : Branchiopoda : Spinicaudata), in eastern Australia

The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.

Diversity and distribution of Laonice species (Annelida: Spionidae) in the tropical North Atlantic and Puerto Rico Trench

Laonice Malmgren, 1867 (Annelida: Spionidae) is a common polychaete genus in the deep-sea. Although most species are quite well studied morphologically, fragmentation and other damage that occurs during sampling often hampers morphological species identification of deep-sea specimens. In this study, we employ three molecular markers (16S, COI and 18S) to study the biodiversity and the distribution patterns of Laonice from the tropical North Atlantic and the Puerto Rico Trench. Based upon different molecular analyses (Automated Barcode Gap Discovery, pairwise genetic distances, phylogenetics, haplotype networks) we were able to identify and differentiate eight Laonice species. Up to four of these species co-occurred sympatrically at the same station. The majority of species were found at multiple stations and two species in the eastern as well as western Atlantic had ranges of up to 4,000 km. Genetic differentiation across these extensive geographic distances was very low. Surprisingly, one 16S haplotype was shared between individuals 2,776 km apart and individuals from the Caribbean and the abyssal plain in the eastern Atlantic (>3,389 km) differed in only a single mutation in 16S. Our results suggest that members of this genus successfully disperse across large geographic distances and are largely unaffected by topographic barriers.

DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Genetic diversity in cytochrome c oxidase I gene of Anopheles mosquitoes

Genetic diversity in cytochrome c oxidase I (coxI) among 7 species of Anopheles mosquitoes from Pakistan, and 37 species from different geographical regions of the world, was recorded. Automatic Barcode Gap Discovery (ABGD) analysis revealed a clear gap between intraspecific and interspecific distances of 7 species from Pakistan. However, genetic distances of 37 Anopheles species failed to adequately differentiate species in a global context. Intraspecific and interspecific divergences for 7 Anopheles species of Pakistan varied from 0.0% to 2.5% (mean = 0.49%) and 8% to 22.3% (mean = 12.77%), respectively. Similarly, intraspecific distances for 37 species from different parts of world ranged from 0.0% to 11.2% (mean = 0.65%) while values of interspecific divergences ranged from 3.4% to 35% (mean = 11.75%). Although phylogenetic tree revealed separate clades for 7 Anopheles species of Pakistan, it failed to produce separate clades for 37 species of the world. It is concluded that although standard barcode region is helpful for identifying Anopheles mosquitoes, combination of multi-locus approaches and morphology may be required to accurately identify species in this genus.

Mating behaviour in laevicaudatan clam shrimp (Crustacea, Branchiopoda) and functional morphology of male claspers in a phylogenetic context: a video-based analysis

Clam shrimps are freshwater branchiopod crustaceans which often present complicated breeding systems including asexual reproduction (parthenogenesis) and mixed mating systems (in androdioecious species both selfing and outcrossing occurs due to the co-presence of hermaphrodites and males). Reproductive patterns of Spinicaudata, which contains most clam shrimp species, have received much attention. Another group of clam shrimps, Laevicaudata, which holds a key position in branchiopod phylogeny, has practically not been studied. As a part of the mating process, males clasp to the carapace margin of the females with a pair (or two pairs) of anterior trunk limbs modified as claspers. Previous studies have shown that clasper morphology is important in a phylogenetic context, and that some parts of the claspers in Spinicaudata and Laevicaudata may have undergone a remarkable parallel evolution. Here we have used video microscopy to study aspects of the mating behaviour, egg extrusion, and fertilization in Lynceus brachyurus (Laevicaudata). It is shown that fertilization is likely to be external and that the peculiar tri-lobed lateral lamellae of female's hind body assist in guiding the egg mass to the exopodal egg carriers where they are collected by their distal setation. The functional morphology of the male claspers was studied in detail by close-up video recordings. The movable "finger" of the clasper bends around the female's carapace edge and serves to hold the female during mating. The larger palp grasps around the female carapace margin in a way very similar to the movable "finger", possibly indirectly providing sensory input on the "finger" position. A brief comparative study of the claspers of a spinicaudatan clam shrimp showed both similarities and differences to the laevicaudatan claspers. The presence of two pairs of claspers in Spinicaudata seems to give males a better hold of the female which may play a role during extended mate guarding.

Cyclestheria hislopi (Crustacea: Branchiopoda): a group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian-Australian lineage, with the latter diverging further in the Paleogene. Today's circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.

Flying with the birds? Recent large-area dispersal of four Australian Limnadopsis species (Crustacea: Branchiopoda: Spinicaudata)

Temporary water bodies are important freshwater habitats in the arid zone of Australia. They harbor a distinct fauna and provide important feeding and breeding grounds for water birds. This paper assesses, on the basis of haplotype networks, analyses of molecular variation and relaxed molecular clock divergence time estimates, the phylogeographic history, and population structure of four common temporary water species of the Australian endemic clam shrimp taxon Limnadopsis in eastern and central Australia (an area of >1,350,000 km(2)). Mitochondrial cytochrome c oxidase subunit I sequences of 413 individuals and a subset of 63 nuclear internal transcribed spacer 2 sequences were analyzed. Genetic differentiation was observed between populations inhabiting southeastern and central Australia and those inhabiting the northern Lake Eyre Basin and Western Australia. However, over large parts of the study area and across river drainage systems in southeastern and central Australia (the Murray-Darling Basin, Bulloo River, and southern Lake Eyre Basin), no evidence of population subdivision was observed in any of the four Limnadopsis species. This indicates recent gene flow across an area of ∼800,000 km(2). This finding contrasts with patterns observed in other Australian arid zone taxa, particularly freshwater species, whose populations are often structured according to drainage systems. The lack of genetic differentiation within the area in question may be linked to the huge number of highly nomadic water birds that potentially disperse the resting eggs of Limnadopsis among temporary water bodies. Genetically undifferentiated populations on a large geographic scale contrast starkly with findings for many other large branchiopods in other parts of the world, where pronounced genetic structure is often observed even in populations inhabiting pools separated by a few kilometers. Due to its divergent genetic lineages (up to 5.6% uncorrected p-distance) and the relaxed molecular clock divergence time estimates obtained, Limnadopsis parvispinus is assumed to have inhabited the Murray-Darling Basin continuously since the mid-Pliocene (∼4 million years ago). This means that suitable temporary water bodies would have existed in this area throughout the wet-dry cycles of the Pleistocene.