Integrative taxonomy aims to document biodiversity by incorporating all useful characters to increase confidence in hypotheses about phylogenetic relationships. In this study, we combine data obtained independently from morphology, two maternally inherited mtDNA genes and two biparentally inherited nuDNA genes to make phylogenetic and taxonomic hypotheses about the Palaearctic members of the bat genus Eptesicus (Vespertilionidae). This genus is distributed worldwide (except for Antarctica) and is highly diversified, presenting one of the most entangled taxonomic puzzles among all mammals. Our results support restoring the genus Rhyneptesicus and separating E. isabellinus and E. pachyomus from E. serotinus and E. ognevi and E. anatolicus from E. bottae. Differences in the phylogenetic hypotheses from mtDNA and nuDNA data suggest the occurrence within E. serotinus of evolutionary processes such as mtDNA capture and secondary contacts between partially differentiated ecomorphs. These two evolutionary processes deserve more in-depth studies within the group.

Despite likely being the most diverse group within the Tricladida, the systematics of land planarians (Geoplanidae) has received minor attention. The most species-rich ingroup, the subfamily Geoplaninae, is restricted to the Neotropics. The systematics of Geoplaninae remains uncertain. Unique features supporting the genera are scanty; moreover, parts of the known species have been poorly described, making comparative studies difficult. Likewise the evolutionary relationships among land planarians remain insufficiently understood. In the present study, a phylogenetic hypothesis for selected taxa of Geoplaninae based on the molecular data is presented and discussed in the light of morphological features. Our phylogenetic inference is based on the fragments of three nuclear regions (18S, 28S rDNA and EF-1α) and a mitochondrial marker (cytochrome oxidase I) for which we considered three optimality criteria (parsimony, maximum likelihood and Bayesian inference). Although our data provide little support for most basal nodes, our phylogenetic trees show a number of well-supported clades, unveiling morphologically homogeneous groups. According to these results, we propose to separate Geoplana into Barreirana (formerly considered a subgenus), Cratera gen. n., Imbira gen. n., Matuxia gen. n., Obama gen. n. and Paraba gen. n., emend the diagnoses of Barreirana, Geoplana, Notogynaphallia, Pasipha and Xerapoa and review the classification of the species within these genera. For Geoplana goetschi sensu Marcus, (1951), a new name is proposed.

We describe a new species, Semispathidium breviarmatum sp. n., from tropical Africa and analyse its phylogenetic position within the subclass Haptoria, using live observation, various silver impregnation methods, SEM and the 18S rRNA gene. Semispathidium breviarmatum differs from its congeners by the much higher number of ciliary rows and by the shape and size of the extrusomes, that is, extrusive organelles that kill the prey. The phylogenetic position of Semispathidium is controversial due to its ‘hybrid’ morphology. Specifically, the cylindroidal body has a more or less discoidal oral bulge indicating an enchelyodonid origin, while the anteriorly curved somatic kineties suggest a spathidiid ancestor. In order to reconstruct the evolutionary history of Semispathidium and to unravel its affinity to other haptorians, we used synergistic effects of combining morphological and molecular data coming from 34 haptorian taxa. These analyses show that Semispathidium belongs to the order Spathidiida representing a basal lineage that is far from ordinary Spathidium species, but very likely related to Protospathidium and Enchelys. Any closer phylogenetic relationship between Semispathidium and Enchelyodon spp. is not recognized in morphological and molecular phylogenies and is consistently excluded by statistical tree topology tests.

In this study, we clarify the relationships between the basal lineages in the moth family Noctuidae using DNA sequence data from eight independent gene regions. Data matrices (6.4 kbp) are analysed using parsimony and model-based methods (maximum likelihood and Bayesian inference). Our results support the family Noctuidae as a monophyletic group in which most subfamilies have hindwing vein M2 reduced or absent. Our phylogenetic hypothesis suggests that in the Noctuidae, the plesiomorphic condition is that in which vein M2 arises about one-third of the way up the discocellular vein between the origins of M1 and M3, mainly parallel to M3, and is of thickness similar to vein M3. Most Noctuidae lineages possess an apomorphic (derived) condition in which hindwing vein M2 is markedly reduced or totally absent, so that the cubital vein appears to be three-branched and these lineages are hence referred to as ‘trifine’. However, Noctuidae also include a number of lineages in which vein M2 is unreduced, or only slightly reduced, and these are more problematic for morphological association with the family Noctuidae. Our results also show that the subfamily Acronictinae is not closely related to Pantheinae, but instead shows a closer association with Amphipyrinae. Among the major lineages of Noctuidae, we postulate a general trend, with numerous exceptions, in larval host plants from woody plants in the basal groups towards herb feeding in derived groups. Similarly, the major radiations of monocot-feeding groups within the family Noctuidae are in the higher trifines. The following taxonomic changes are proposed: Thiacidinae, syn. nov., a junior synonym of Pantheinae, and Dyopsinae, stat. nov., are reinstated as a subfamily.

Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly of Osteocephalus with respect to Tepuihyla, (ii) the placement of ‘Hyla’ warreni as sister to Tepuihyla, (iii) the non-monophyly of several currently recognized species within Osteocephalus and (iv) the presence of low (<1%) and overlapping genetic distances among phenotypically well-characterized nominal species (e.g. O. taurinus and O. oophagus) for the 16S gene fragment used in amphibian DNA barcoding. We propose a new taxonomy, securing the monophyly of Osteocephalus and Tepuihyla by rearranging and redefining the content of both genera and also erect a new genus for the sister group of Osteocephalus. The colouration of newly metamorphosed individuals is proposed as a morphological synapomorphy for Osteocephalus. We recognize and define five monophyletic species groups within Osteocephalus, synonymize three species of Osteocephalus (O. germani, O. phasmatus and O. vilmae) and three species of Tepuihyla (T. celsae, T. galani and T. talbergae) and reallocate three species (Hyla helenae to Osteocephalus, O. exophthalmus to Tepuihyla and O. pearsoni to Dryaderces gen. n.). Furthermore, we flag nine putative new species (an increase to 138% of the current diversity). We conclude that species numbers are largely underestimated, with most hidden diversity centred on widespread and polymorphic nominal species. The evolutionary origin of breeding strategies within Osteocephalus is discussed in the light of this new phylogenetic hypothesis, and a novel type of amplexus (gular amplexus) is described.

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention and control strategies. Flat mites of the Brevipalpus genus include several crop pests and the systematics of these mites represents a challenge for acarologists. Many of the most economically important Brevipalpus species have repeatedly been inaccurately identified. Such problematic classification has been attributed to the likely occurrence of cryptic species in the genus. In this study, we used an integrative approach that combined molecular analyses, including sequence-based species delimitation, with detailed morphological identification using traits that have recently showed to be taxonomically informative. Sequences of mitochondrial cytochrome c oxidase subunit I (COI) were obtained from individuals collected from host plants belonging to 14 genera and 13 families across 29 locations in the Americas (Brazil, Chile, USA). The phylogenetic analyses included previously published Brevipalpus sequences from GenBank, and the final data set was classified into 44 haplotypes. Six putative species were recognised by COI-based species delimitation analysis, and morphological evidence supported each of these species. The integrative approach revealed the occurrence of cryptic species in the Brevipalpus genus and contributed to the clarification of previously noted incongruences. The results presented here allow for the evaluation of taxonomic characteristics in a phylogenetic context and indicate new characters for the differentiation of Brevipalpus species. In addition, Brevipalpus incognitus n. sp. Ferragut & Navia, a cryptic species detected in this study, is described based on morphological and molecular traits. Implications of the advances in Brevipalpus systematics presented herein with respect to pest management are briefly discussed.

Grass snakes (Natrix natrix) represent one of the most widely distributed snake species of the Palaearctic region, ranging from the North African Maghreb region and the Iberian Peninsula through most of Europe and western Asia eastward to the region of Lake Baikal in Central Asia. Within N. natrix, up to 14 distinct subspecies are regarded as valid. In addition, some authors recognize big-headed grass snakes from western Transcaucasia as a distinct species, N. megalocephala. Based on phylogenetic analyses of a 1984-bp-long alignment of mtDNA sequences (ND4+tRNAs, cyt b) of 410 grass snakes, a nearly range-wide phylogeography is presented for both species. Within N. natrix, 16 terminal mitochondrial clades were identified, most of which conflict with morphologically defined subspecies. These 16 clades correspond to three more inclusive clades from (i) the Iberian Peninsula plus North Africa, (ii) East Europe and Asia and (iii) West Europe including Corso-Sardinia, the Apennine Peninsula and Sicily. Hypotheses regarding glacial refugia and postglacial range expansions are presented. Refugia were most likely located in each of the southern European peninsulas, Corso-Sardinia, North Africa, Anatolia and the neighbouring Near and Middle East, where the greatest extant genetic diversity occurs. Multiple distinct microrefugia are inferred for continental Italy plus Sicily, the Balkan Peninsula, Anatolia and the Near and Middle East. Holocene range expansions led to the colonization of more northerly regions and the formation of secondary contact zones. Western Europe was invaded from a refuge within southern France, while Central Europe was reached by two distinct range expansions from the Balkan Peninsula. In Central Europe, there are two contact zones of three distinct mitochondrial clades, and one of these contact zones was theretofore completely unknown. Another contact zone is hypothesized for Eastern Europe, which was colonized, like north-western Asia, from the Caucasus region. Further contact zones were identified for southern Italy, the Balkans and Transcaucasia. In agreement with previous studies using morphological characters and allozymes, there is no evidence for the distinctiveness of N. megalocephala. Therefore, N. megalocephala is synonymized with N. natrix.

Based on phylogenetic and molecular dating analyses of several species of Cnemidophorus and Ameiva, representing major groups of species of these two genera, we uncover a previously unrecognized Ameiva lineage, which includes described Cnemidophorus parecis from south-western Amazonia. We discuss the diagnosis of Ameiva and Cnemidophorus and the implications of the new taxonomic rearrangement of genera from Teiidae for the monophyly of Ameiva. Based on the conclusion of our analyses, we provide description of a new species named Ameiva jacuba from the central Brazilian Cerrado and a detailed diagnosis for the relocation of C. parecis to Ameiva. We do not adopt here recent taxonomic changes proposed for Teiidae and provide a discussion about them. Finally, based on molecular dating and the distribution of living species, we propose an evolutionary scenario for the origins of South American cis-Andean Ameiva lineages, associated with the topographic subdivision of the Cerrado region during Miocene marine introgressions.

In an effort to evaluate the four Akodon species groups, phylogenetic relationships among individuals of the genus Akodon, selected from throughout South America, were examined using cytochrome b and a concatenated data set consisting of data from cytochrome b, exon 6 of the dentin matrix protein 1 and the nuclear intron thyrotropin. Both the cytochrome b data set and the combined data set were analysed under maximum parsimony, maximum likelihood and Bayesian criteria. Like previous studies, a monophyletic Akodon clade was recovered. Monophyly of the boliviensis and cursor groups was supported, and the two form a strongly supported sister relationship. Akodon azarae is basal to and forms a monophyletic group with the boliviensis + cursor clade, resolving the placement of A. azarae but leaving it unassignable to a current Akodon species group. The aerosus and varius groups are paraphyletic as four members of the varius group (A. glaucinus, A. simulator, A. tartareus and A. varius) fall within the aerosus group. Akodon lindberghi is formally placed in the cursor group. Akodon caenosus is recognized as a species distinct of A. lutescens, A. orientalis is recognized as a species distinct of A. orophilus, and A. aerosus, A. baliolus and A. surdus are recognized as three separate species. Based upon chronophylogenetic analysis, the initial divergence within Akodon likely began during the late Pliocene and ancestors of the four extant species groups (aerosus, boliviensis, cursor and dolores) appeared around the Pleistocene–Pliocene boundary or shortly thereafter.

The complete larval series (zoea I, zoea II and megalopa) of the crab Ergasticus clouei is described and illustrated based on plankton samples from Mediterranean waters. The zoea II and megalopal stages, previously unknown, are described here for the first time. Nucleotide sequence analysis of two gene regions (16S rDNA and Cox1 genes) confirmed the assignment of these larvae to Ergasticus clouei. The molecular analyses and the morphology of the larval stages revealed large differences between Ergasticus and Inachus, the type genus of the family Inachidae. In fact, E. clouei larvae presented a series of morphological characters, such as antennal shape and mouthparts setation pattern that placed them closer to the family Oregoniidae. The phylogenetic analyses also showed significant support for the monophyly of the Oregoniidae + Ergasticus group. The data argue for removal of Ergasticus and the related genera (Bothromaia, Pleisticanthoides, Parapleisticantha and Pleistacantha) from the Inachidae and their placement within the Oregoniidae as a separate subfamily, Pleistacanthinae Števčić, 2005. Our results demonstrate that larval stages provide reliable morphological traits, independent from those of adults, to help resolving relationships among Majoidea genera.

We comprehensively revise the taxonomy of the camaenid genus Mesodontrachia Solem, 1985, which is endemic to the Victoria River District and East Kimberley in the north-western Australian Monsoon Tropics based on comparative analyses of key morphological features and mitochondrial DNA sequences. We examined newly collected samples from several collection sites spread over nearly 20 000 km² of mostly inaccessible land, which represented all three currently known and three previously undescribed species. All species were initially identified as members of Mesodontrachia based on their similar, putatively typical shell. However, Mesodontrachia as so delimited was polyphyletic in a mitochondrial phylogeny with respect to several other camaenid genera from NW Australia. Contrary to the shell, we found considerable variation in the penial anatomy that was consistent with the mtDNA differentiation. To retain monophyletic taxa, we propose a revised taxonomy whereby Mesodontrachia is maintained as a monotypic taxon. In addition, four genera (Nodulabium, Ototrachia, Pseudomesodontrachia and Vincentrachia) and three species (P. gregoriana, O. compressa and N. solidum) are newly described. The shell of all these taxa is highly conserved and of little taxonomic utility. Shell similarity is attributed to a similar life style in a similar and harsh environment.

Lebedev, V.S., Bannikova, A.A., Pagès, M., Pisano, J., Michaux, J.R. & Shenbrot, G.I. (2012). Molecular phylogeny and systematics of Dipodoidea: a test of morphology-based hypotheses. —Zoologica Scripta, 42, 231–249.

Here, we present a comprehensive phylogenetic analysis based on nuclear and mitochondrial DNA sequences of rodents of the subfamily Sigmodontinae. The emphasis is placed on the large tribe Phyllotini; sampling includes for the first time in any molecular-based phylogenetic analysis representatives of several genera traditionally considered to be phyllotines. Given the broad taxonomic sampling, results provide substantial improvements in our knowledge on both the structure of the sigmodontine radiation and of phyllotine phylogenetic relationships. For instance, the tribe Ichthyomyini was not recovered monophyletic. Similarly, in a novel hypothesis on the contents of the tribe Phyllotini, it is shown that unlike Galenomys, the genera Chinchillula, Neotomys and Punomys are not phyllotines. The later genera together with Andinomys, Euneomys, Irenomys and Juliomys form part of novel generic clades of mostly Andean sigmodontine rodents. More in general, results strongly suggest the occurrence of several instances of putative morphological convergence among distinct sigmodontine lineages (e.g. among now considered to be ichthyomyines; between Phyllotini and some Andean taxa; among Euneomys-Neotomys and Reithrodon). Finally, we suggest that the historical biogeography of the sigmodontine rodents is far more complex than earlier envisioned.

The diverse group of Asian wolf snakes of the genus Lycodon represents one of many poorly understood radiations of advanced snakes in the superfamily Colubroidea. Outside of three species having previously been represented in higher-level phylogenetic analyses, nothing is known of the relationships among species in this unique, moderately diverse, group. The genus occurs widely from central to Southeast Asia, and contains both widespread species to forms that are endemic to small islands. One-third of the diversity is found in the Philippine archipelago. Both morphological similarity and highly variable diagnostic characters have contributed to confusion over species-level diversity. Additionally, the placement of the genus among genera in the subfamily Colubrinae remains uncertain, although previous studies have supported a close relationship with the genus Dinodon. In this study, we provide the first estimate of phylogenetic relationships within the genus Lycodon using a new multi-locus data set. We provide statistical tests of monophyly based on biogeographic, morphological and taxonomic hypotheses. With few exceptions, we are able to reject many of these hypotheses, indicating a need for taxonomic revisions and a reconsideration of the group's biogeography. Mapping of color patterns on our preferred phylogenetic tree suggests that banded and blotched types have evolved on multiple occasions in the history of the genus, whereas the solid-color (and possibly speckled) morphotype color patterns evolved only once. Our results reveal that the colubrid genus Dinodon is nested within Lycodon—a clear finding that necessitates the placing of the former genus in synonymy with the latter.

The bivalve family Corbulidae, known colloquially as ‘basket clams’, includes species tolerating a wide variety of habitats ranging from open marine to freshwater. Previous studies of corbulid phylogenetics have been based mainly on shell morphology and to some extent soft tissue anatomy. However, these studies have been inadequate for corbulid classification because of difficulties in determining the inter-relationships of primarily marine species with non-marine species, the latter commonly exhibiting highly divergent morphological, ecological and environmental characteristics from their marine counterparts. The first molecular phylogenetic study of the Corbulidae is presented herein, analysing DNA sequences from the 18S rRNA and 28S rRNA genes, separately and in combination. Fifteen corbulid species and 14 outgroup taxa were included in the analyses. Corbulidae is resolved as monophyletic, comprising three groups with varying support. The non-marine species form one group that we name as the subclade ‘limnetic–euryhaline Corbulidae’ (LEC) and comprising the genera Lentidium, Erodona and Potamocorbula. This LEC, which is consistently recovered as monophyletic, is globally distributed. The marine Corbulidae are divided into two well-supported lineages in combined analyses although there are inconsistencies in their membership between single-gene analyses. One of the two lineages consists of primarily Western Pacific taxa and the other of North American and Caribbean taxa. Finally, the authors advocate further study on the LEC to mitigate potential biological invasions beyond their native distribution.

Vujić, A., Ståhls, G., Ačanski, J., Bartsch, H., Bygebjerg, R. & Stefanović, A. (2013). Systematics of Pipizini and taxonomy of European Pipiza Fallén: molecular and morphological evidence (Diptera, Syrphidae). —Zoologica Scripta, 42, 288–305.

Ainscough, B.J., Breinholt, J.W., Robison, H.W. & Crandall, K.A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). —Zoologica Scripta, 42, 306–316.

Jorgensen, M. C., Sierwald, P. & Mason-Gamer, R. J. (2012). A review of subspecies recognition in polydesmidan millipedes (Diplopoda) with a revision of the subspecies of Euryuridae (Xystodesmoidea). —Zoologica Scripta, 42, 317–326.

Marie-Stephane, T. (2012). Statistical approaches for morphological continuous characters: a conceptual model applied to Phytoseiidae (Acari: Mesostigmata). —Zoologica Scripta, 42, 327–334.