Geographical differentiation and cryptic diversity in the monocled cobra,Naja kaouthia (Elapidae), from Thailand

South‐East Asia has an exceptionally high diversity of snakes, with more than 250 snake species currently recorded from Thailand. This diversity likely reflects the diverse range of geographical and climatic conditions under which they live, but the evolutionary history and population genetics of many snake species in South‐East Asia have been little investigated in comparison with morphological studies. Here, we investigated genetic variation in the monocled cobra, Naja kaouthia, Lesson, 1831, across its distribution range in Thailand using mitochondrial DNA (cytochrome b, control region) for ~100 individuals and the nuclear DNA gene (C‐mos) for a small subset. Using population genetic and phylogenetic methods, we show high levels of genetic variation between regional populations of this non‐spitting cobra, including the north‐eastern, north‐central and southern regions, in addition to a population on Pha‐ngan Island, 150 km offshore from the southern peninsula. Moreover, inclusion of the north‐eastern population renders N. kaouthia paraphyletic in relation to other regional Naja species. The north‐eastern population is therefore probably specifically distinct. Given that these cobras are otherwise undifferentiated based on colour and general appearance to the “typical” cobra type of this region, they would represent a cryptic species. As has been shown in other animal groups from Thailand, it is likely that the geographical characteristics and/or tectonic alteration of these regions have facilitated high levels of population divergence of N. kaouthia in this region. Our study highlights the need for dense sampling of snake populations to reveal their systematics, plan conservation and facilitate anti‐snake venom development.     

Ontogeny of the chondrocranium in Corydoras aeneus (Gill, 1858) (Callichthyidae, Siluriformes)

Callichthyids take a basal position in the loricarioid evolutionary lineage leading up to an algae scraping feeding mechanism in the loricariid family. Therefore, the study of the morphology and development of a callichthyid representative would contribute to a better knowledge on the differences in cranial morphology and their impact on feeding ecology within this superfamily. Therefore, development in the chondrocranium of Corydoras aeneus was studied based on 22 cleared and stained specimens and 6 series of serial sections. The latter sections were also digitized and used for 3D reconstructions. Development overall follows the typical siluriform trends in chondrocranial development. Even the low complexity of the chondrocranium at hatching fits the trend observed in other siluriforms, although other studies showed loricarioid hatchlings to generally show more complex chondrocrania. In contrast to other catfish, in C. aeneus, the notochord was never found to protrude into the hypophyseal fenestra. In addition, also differing from other siluriforms, a commissura lateralis is present, a state also reported for Ancistrus cf. triradiatus (Geerinckx et al., [2005] J Morphol 266:331-355). The splanchnocranium again has the typical siluriform shape during its ontogeny, with the presence of a compound hyosymplectic-pterygoquadrate plate, although not fused to the neurocranium or interhyal at any time during ontogeny, a state described earlier for Callichthys callichthys (Hoedeman, [1960a] Bull Aquat Biol 1:73-84; Howes and Teugels, [1989] J Zool Lond 219:441-456). The most striking difference found in comparison to other catfishes, however, involves thebranchial basket, which arises as a single element with a further differentiation from the middle arches on in both a rostral and caudal direction.     

Extensive chromosomal rearrangements and nuclear DNA content changes in the evolution of the armoured catfishes genus Corydoras (Pisces, Siluriformes, Callichthyidae)

Karyotypes and nuclear DNA content were studied in 11 species of the genus Corydoras from rivers in South America: C . sp. from Caripi river 2 n =60, C . cf. simulatus 2 n =62, C . simulatus 2 n =62, C . reticulatus 2 n =74, C . sp. from Galheiro river 2 n =84, C . aff. punctatus from Negro river 2 n =102, C . flaveolus 2 n =58, C . arcuatus 2 n =46, C . trilineatus 2 n =46, C . schwartzi 2 n =46, and C . metae 2 n =92. Extensive chromosome diversity and differences in DNA content were detected among species. The high variability in chromosome counts was not exclusively related to chromosomal structural rearrangements, but also to large changes in DNA content. Species could be grouped using their shared cytogenetic characteristics, suggesting that within the genus Corydoras different groups of species followed distinct evolutionary trends. Chromosomal rearrangements in Corydoras are, apparently, more frequent that morphological modifications, so cytogenetic data may be very useful for species delimitation and for the understanding of interrelationships among species.     

Variation of male reproductive apparatus in relation to fertilization modalities in the catfish families Auchenipteridae and Callichthyidae (Teleostei: Siluriformes)

To investigate the relationship between fertilization modalities and the morphology of male reproductive apparatus, two species of Auchenipteridae, Auchenipterus nuchalis and Tatia intermedia , and six species of Callichthyidae, Callichthys callichthys , Corydoras aeneus , Corydoras bondi , Corydoras ehrhardti , Corydoras potaroensis and Hoplosternum littorale were studied. The species analysed show either internal or external fertilization, the latter including the so called 'sperm drinking' type of mating. An anal fin modified as an intromittent organ, a pair of seminal vesicles, and the release of sperm in the form of discrete bundles (spermatozeugmata) characterize the male reproductive apparatus of the internal fertilizer A. nuchalis . Seminal vesicles are present also in C. aeneus , C. bondi , C. ehrhardti , C. potaroensis and H. littorale , species performing 'sperm drinking' spawning. In contrast, regardless of the family, species showing the more classic type of external fertilization lack specialized accessory organs. Where occurring, the major function of seminal vesicles is the secretion of mucins. The role of these mucosubstances, in relation to spermatozeugmata formation, in internal fertilizers, or the protection of sperm passing through the female gut, in the 'sperm-drinking' species, is discussed. Variation, between families, in the shape of testis and accessory structures, as well as in the type of spermatogenesis was found. Neither the reproductive modalities nor the phylogenetic relationships, however, appear to fully account for these differences.     

Phylogeographic analysis of the brooding brittle star Amphipholis squamata (Echinodermata) along the coast of New Zealand reveals high cryptic genetic variation and cryptic dispersal potential

Abstract.— Direct development in benthic marine invertebrates is usually associated with narrow geographical range, low rates of colonization, and low levels of gene flow. Paradoxically, the small brittle star Amphipholis squamata broods its larvae to a crawl-away juvenile stage, yet has a cosmopolitan distribution. Using sequence and restriction-fragment-length-polymorphisms (RFLP) analyses of nuclear and mitochondrial DNA from 16 coastal populations throughout New Zealand, we tested whether the species is indeed a poor disperser, as may be expected from its brooding habit. We predicted that local and regional populations would be genetically structured according to isolation by distance. We also suspected that this ubiquitous "species" is composed of a variety of cryptic taxa in different geographic areas, as has been discovered in an increasing number of marine invertebrates. We found evidence of four genetically divergent and reproductively isolated lineages that can exist in syntopy. Lineages vary in abundance, haplotype diversity, and geographic distribution. The partitioning of genetic variation within the most common lineage, as well as the geographic distribution of the four lineages, suggest a north/south split. This pattern is consistent with known New Zealand marine biogeographic zones and appears to be linked to the regime of oceanic circulation, which is characterized by subtropical, southward-moving water masses in the north, and sub-Antarctic, northward-moving water in the south. We conclude that the dispersal ability of A. squamata is regionally restricted but with sporadic long-distance dispersal, which serves to increase local genetic variation. Our results support the idea that dispersal occurs through passive transport by drifting or rafting on macroalgae, which A. squamata commonly inhabits, and emphasize that poor dispersal ability is not necessarily a corollary of direct development.     

Mitochondrial DNA sequences reveal extensive cryptic diversity within a western American springsnail

We analysed cytochrome c oxidase subunit I and NADH dehydrogenase subunit I sequence variation among 29 populations of a widely ranging southwestern springsnail (Pyrgulopsis micrococcus) and 18 regional congeners. Cladistic analyses of these sequences depict P. micrococcus as a polyphyletic composite of five well-supported clades. Sequence divergences among these clades and subclades imply the possible occurrence of as many as seven or eight cryptic species in addition to P. micrococcus. Our finding that P. micrococcus contains multiple, genetically distinct and geographically restricted lineages suggests that diversification within this highly speciose aquatic genus has been structured in large part by the operation of terrestrial barriers to gene flow. However, these sequence data also indicate that recent dispersal among hydrographically separated areas has occurred within one of these lineages, which we attribute to passive transport on migratory waterbirds.     

Revisiting the phylogeography of Asellus aquaticus in Europe: insights into cryptic diversity and spatiotemporal diversification

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Global diversity and biogeography of Skeletonema species (bacillariophyta)

Recent studies have shown that the cosmopolitan diatom Skeletonema costatum sensu lato is composed of several morphologically and genetically distinct species. To assess whether the separate species have a cosmopolitan distribution, we analysed 184 strains from marine and estuarine sites worldwide. We identified the strains using light and electron microscopy, and we sequenced the hyper-variable region of nuclear LSU rDNA. All recently described species were genetically distinct, and all but two were morphologically distinct. Variability was found for the only ultrastructural character used to distinguish Skeletonema dohrnii and S. marinoi, which cannot be identified based on morphology alone. Furthermore, multiple genetically distinct taxa, which may represent cryptic species, were found within the S. menzelii and S. tropicum clades. We found that all currently recognized species of Skeletonema are widespread, however, gaps seem to occur in their geographical ranges. For example, some species are found in both the northern and southern temperate latitudes whereas other species appear to have only subtropical to tropical ranges. Skeletonema pseudocostatum and S. grethae seem to have more restricted geographical ranges because the former was not found along American coasts and the latter was encountered only in US waters. A taxonomic update is provided for Skeletonema strains currently available in several culture collections, which could aid reinterpretation of results obtained in comparative studies using these strains.     

Deep genetic divergence in the darkling beetle Pimelia rugulosa (Coleoptera,Tenebrionidae) reflects Plio‐Pleistocenic paleogeographic history of Sicily

The genus Pimelia is represented in Sicily by the two species P. grossa and P. rugulosa, the latter with the two subspecies P. r. rugulosa and P. r. sublaevigata. A third subspecies, P. r. apula, is present only in Puglia. The phylogeographic history of this genus in Sicily was reconstructed using sequences of the complete cox2 gene, applying phylogenetic and molecular dating methods. Phylogenetic analysis confirmed the monophyly of the two species, as well as the subdivision of P. rugulosa in the three morphological subspecies. One previously undetected and deeply divergent lineage was described that is geographically related to the Hyblean massif. It is therefore suggested that the deep divergence of the two major P. rugulosa clades in Sicily reflects an ancient separation between the Hyblean massif and the other land masses of Sicily. Dating analysis confirmed that the timing of P. rugulosa genetic divergence is compatible with the formation of the Hyblean massif. Furthermore, P. rugulosa populations of the Hyblean massif, whose taxonomy has been historically problematic, display levels of genetic divergence comparable to those observed at the species level. The possibility that this new lineage might deserve species rank is presented.     

Molecular data illuminate cryptic nudibranch species: the evolution of the Scyllaeidae (Nudibranchia: Dendronotina) with a revision of Notobryon

Scyllaeidae represents a small clade of dendronotoid nudibranchs. Notobryon wardi Odhner, 1936, has been reported to occur in tropical oceans from the Indo‐Pacific and eastern Pacific to temperate South Africa. The systematics of Notobryon has not been reviewed using modern systematic tools. Here, specimens of Notobryon were examined from the eastern Pacific, the Indo‐Pacific, and from temperate South Africa. Additionally, representatives of Scyllaea and Crosslandia were studied. Scyllaeidae was found to be monophyletic. Notobryon was also found to be monophyletic and is the sister group to Crosslandia plus Scyllaea. The molecular data also clearly indicate that within Notobryon, at least three distinct species are present, two of which are here described. Genetic distance data indicate that eastern Pacific and South African exemplars are 10–23% divergent from Indo‐Pacific exemplars of Notobryon wardi. Scyllaea pelagica has been regarded as a single, circumtropical species. Our molecular studies clearly indicate that the Atlantic and Indo‐Pacific populations are distinct and we resurrect Scyllaea fulva Quoy & Gaimard, 1824 for the Indo‐Pacific species. Our morphological studies clearly corroborate our molecular findings and differences in morphology distinguish closely related species. Different species clearly have distinct penial morphology. These studies clearly reinforce the view that eastern Pacific, Indo‐Pacific, and temperate biotas consist largely of distinct faunas, with only a minor degree of faunal overlap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 311–336.     

Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae)

The geographic distributions of marine fishes have been shaped by ancient vicariance and ongoing dispersal events. Some species exhibit anti‐equatorial distributions, inhabiting temperate regions on both sides of the tropics while being absent from equatorial latitudes. The perciform fish Microcanthus strigatus (the stripey) exhibits such a distribution with disjunct populations occurring in East Asia, Hawaii, Western Australia, and the southwest Pacific. Here, we examine the historical biogeography and evolutionary history of M. strigatus, based on more than 80 specimens sampled from the four major populations. We analysed 36 morphological characters, three mitochondrial markers, and two sets of 7,120 and 12,771 single‐nucleotide polymorphisms from the nuclear genome. Our results suggest that M. strigatus represents a cryptic species complex comprising at least two genetically distinct populations worthy of species‐level recognition, with one population exhibiting strong genetic structuring but with intermittent, historical gene flow. We provide evidence for a southwest Pacific origin for the ancestral Microcanthus and explain how past connectivity between these regions might have given rise to the relationships observed in present‐day marine fauna. Our ancestral range reconstructions and molecular‐clock analyses support a southwest Pacific centre of origin for Microcanthus, with subsequent colonization of Western Australia through the Bass Strait followed by transequatorial dispersals to the Northern Hemisphere during the Pleistocene. Our results detail an anti‐tropical dispersal pattern that is highly unusual and previously undocumented, thereby emphasizing the importance of integrative systematics in the evaluation of widespread species.     

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 23–38.     

Marphysa (Eunicidae,polychaete, Annelida) species of the Sanguinea group from Australia,with comments on pseudo‐cryptic species

The genus Marphysa is widely collected for bait by recreational fishermen in Australia, and yet the number of species remains unresolved. A new species is described together with additional information on a previously described species. This study reveals that while species of Marphysa superficially resemble one another, detailed studies on the distribution of different types of chaetae along the body, together with molecular studies, uncover species which may co‐occur. Correct identification is critical for management of these largely intertidal species. This study also highlights the increasing awareness of the presence of pseudo‐cryptic species in polychaetes.     

DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity

The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and ‘species groups’ within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include ‘species-complexes’ previously considered as a single taxon. Our results revealed the presence of three species groups, ‘C. amplexus’, ‘C. conspicillatus’ and ‘C. haematopterus’ and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.     

Combining molecular, morphological and ecological data to infer species boundaries in a cryptic tropical pitviper

Few operational methods exist for delimiting species boundaries, and these usually require sampling strategies that are unrealistic for widespread organisms that occur at low densities. Here we apply molecular, morphological and ecological species delimitation criteria to a wide-ranging, fragmented group of Asian green pitvipers, the Popeia popeiorum complex. A mitochondrial DNA phylogeny for the group indicates two well-differentiated clades, corresponding mainly to northern and southern parts of its range. Strong phylogeographical structure within each clade suggests isolation in forest refugia during the Pliocene and a southward colonization of the Sunda islands during the Pleistocene. Multivariate analysis of morphological characters reveals a generally conserved pattern of geographical variation, incongruent with the recovered phylogenetic history. We compare groups delineated by mtDNA variation to morphological and ecological divisions in the complex, and discuss the implications of these for the taxonomy of the group. Discordance between species boundaries inferred from different criteria suggests that combining independent sources of data provides the most reliable estimation of species boundaries in organisms that are difficult to sample in large numbers.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 343–364.     

Insight into the phylogeny of African Clariidae (Teleostei, Siluriformes): implications for their body shape evolution, biogeography, and taxonomy

The phylogenetic relationships among Clariidae species (Teleostei, Siluriformes) were assessed using 563 nucleotides of the cytochrome b mitochondrial gene. We included 32 Clariidae species representative of seven genera in our analysis. Hetropneustes fossilis (Heteropneustidae) and Clarotes laticeps (Claroteidae) were used as outgroups. The molecular data identified two evolutionary lineages that correspond on one hand to African species and on the other hand to Asian species. Morphological and osteological evolution in Clariidae did not follow an orthogenetic series. Species with robust body, strong ossified head, and large adipose fin were not ancestral ones and eel-like species were not phylogenetically related and represent independent adaptation to life in mud. Adaptation to life in deep water occurred two times independently in lake Tanganyika (with Dinotopterus cunningtoni) and in Lake Malawi (with Bathyclarias species). Molecular dating using a molecular clock of 1% divergence per million years and a comparison with fossils records allowed an estimate of the timing of cladogenesis within the species studied. The Clariidae family originated in Asia 50 MY ago but contemporary African and Asian studied species originated from a common ancestor that was present on the Arabian plate about 15 MY ago. Systematic implications of these results are also discussed.     

Cryptic diversity, molecular phylogeny and biogeography of the rock- and leaf litter-dwelling land snails of Belau (Republic of Palau, Oceania)

The endemic diplommatinid land snails (Caenogastropoda: Mollusca) of Belau (Republic of Palau, Micronesia) are an exceptionally diverse group of largely undescribed species distributed among rock and leaf litter habitats on most of Belau's 586 islands. Diplommatinid shell morphology (e.g. shell sculpture) reflects habitat type. In this study, I analysed a subset of the 90 diplommatinid species representing a broad geographical spread of islands in order to reveal the species' phylogenetic relationships and biogeography within the Belau archipelago. Diplommatinid species from the islands of Yap, Pohnpei, Kosrae and Guam are also included in the analysis. One nuclear (28S rRNA) and two mitochondrial (16S rRNA, COI) gene regions comprising 1906bp were used for phylogenetic reconstruction. Results show that (i) the Belau Diplommatinidae are not monophyletic, as Guam and Yap species should be included as part of the radiation, (ii) Pohnpei and Kosrae species are highly divergent from Belau diplommatinids, (iii) there is little evidence for in situ radiation within individual Belau islands, (iv) spined and heavily calcified rock-dwelling species form a well-supported clade, and (v) Belau diplommatinid genera are in need of revision.     

An underground burst of diversity – a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Using both nuclear and mitochondrial sequences, we demonstrate high genetic differentiation in the genus Talpa and confirm the existence of cryptic species in the Caucasus and Anatolia, namely, T. talyschensis Vereschagin, 1945, T. ognevi Stroganov, 1948, and Talpa ex gr. levantis. Our data support four clades in the genus Talpa that showed strong geographical associations. The ‘europaea’ group includes six species from the western portion of the genus' range (T. europaea, T. occidentalis, T. romana, T. caeca, T. stankovici, and T. levantis s.l.); another three groups are distributed further east: the ‘caucasica’ group (Caucasus), the ‘davidiana’ group (eastern Anatolia and Elburz) and T. altaica (Siberia). The phylogenetic position of T. davidiana was highlighted for the first time. The order of basal branching remains controversial, which can be attributed to rapid diversification events. The molecular time estimates based on nuclear concatenation estimated the basal divergence of the crown Talpa during the latest Miocene. A putative scenario of Talpa radiation and issues of species delimitation are discussed. © 2015 The Linnean Society of London