An integrative systematic revision of the European southern birch mice (Rodentia: Sminthidae,Sicista subtilis group)

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Molecular analyses of turf algae reveal a new species and an undetected introduction in the Pterosiphonieae (Rhodomelaceae,Rhodophyta)

Introduced seaweeds and undescribed species often remain undetected because marine regional floras are as yet poorly understood. DNA sequencing facilitates their detection, but databases are incomplete, so their improvement will continue to lead the discovery of these species. Here we aim to clarify the taxonomy of two turf-forming red algal Australian species that morphologically resemble the European Aphanocladia stichidiosa. We also aim to elucidate whether either of these species could have been introduced in Europe or Australia. We studied their morphology, analyzed 17 rbcL sequences of European and Australian specimens, examined their generic assignment using a phylogeny based on 24 plastid genomes, and investigated their biogeography using a taxon-rich phylogeny including 52 rbcL sequences of species in the Pterosiphonieae. The rbcL sequences of one of the Australian species were identical to A. stichidiosa from Europe, considerably expanding its known distribution. Unexpectedly, our phylogenetic analyses resolved this species in the Lophurella clade rather than in Aphanocladia and the new combination L. stichidiosa is proposed. The other Australian species is described as L. pseudocorticata sp. nov. Although L. stichidiosa was originally described in the Mediterranean ca. 70 years ago, our phylogenetic analyses placed it in a lineage restricted to the southern hemisphere, showing that it is native to Australia and introduced to Europe. This study confirms that further work using molecular tools is needed to characterize seaweed diversity, especially among the poorly explored algal turfs, and showcases the usefulness of phylogenetic approaches to uncover introduced species and to determine their native ranges.     

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.     

Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

Assessing the diversity and distribution of Cephalothrix species (Nemertea: Palaeonemertea) in European waters by comparing different species delimitation methods

Soft‐bodied marine taxa, like ribbon worms (Nemertea), often lack clear diagnostic morphological characters impeding traditional species delimitation. Therefore, recent studies concentrated on molecular genetic methods to solve taxonomic issues. Different delimitation methods were employed to explore species boundaries and the presence of cryptic species. However, the performance of the different delimitation methods needs to be tested. A particularly promising nemertean genus in this regard is the palaeonemertean genus Cephalothrix that is commonly found in European waters. In order to gain information on the number and distribution of European cephalotrichids and to test different tree‐based and non‐tree‐based delimitation methods, we analyzed a dataset comprising the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) of 215 European Cephalothrix specimens, of which 78 were collected for this study. Our results show the presence of 12–13 European lineages of which several can be assigned to known European species. Analyzing a second dataset comprising 74 additional sequences from the Pacific and the Atlantic Oceans helped identify some of the unassigned European specimens. One resulting clade seems to represent a non‐native introduced Cephalothrix species, while another has never been recorded from Europe before. In our analysis, especially the tree‐based methods and the phylogenetic analysis proved to be a useful tool when delimiting species. It remains unclear whether the different identified clades result from cryptic speciation or from a high genetic variability of the COI gene.     

Phylogeny and species reassessment of Hyalopterus (Aphididae,Aphidinae)

The broadly distributed genus Hyalopterus currently comprises three formally recognized species that are highly similar morphologically and hence difficult to be identified with certainty. This group has undergone multiple revisions in the past century, but none of these has assessed species from Asia, which has hampered our understanding of the species diversity within this genus. Based on a comprehensive data set from morphological data and host-associated data, and by coalescent-based delimitation approaches, the Hyalopterus species boundaries, distribution and diversity were clarified here to further reveal the composition of the species. Two single-locus (ML-GMYC and mPTP) and two multilocus (BPP and STACEY) delimitation methods were conducted based on extensive sampling. Then, the phylogenetic relationships and morphological divergence were assessed. Our data strongly supported that the number of recognized species in Hyalopterus had likely been underestimated. The phylogenetic analyses recovered four major clades, which corresponded to distinct host-plant preferences. Also, the morphological analyses showed significant differentiation for only one of the newly recognized candidate species uncovered by the delimitation approaches, suggesting the existence of at least two independent evolutionary lineages within Hyalopterus arundiniformis, which showed different patterns of host association. Moreover, based on our data, the taxonomic misidentification of H. arundiniformis in China was corrected here. This study lays the groundwork for the thorough taxonomic revision of Hyalopterus and for future evolutionary studies and underlines the importance of an integrated framework for species determination.     

Molecular and morphological diversity in species of Kronichthys (Teleostei,Loricariidae) from Atlantic coastal rivers of Brazil

The Neotropical catfish genus Kronichthys contains three species distributed along coastal rivers of southern and southeastern Brazil. Although phylogenetic hypotheses are available, the molecular and morphological diversity and species boundaries within the genus remain unexplored. In this study, the authors generated mitochondrial data for 90 specimens combined with morphometric and meristic data to investigate species diversity, species boundaries and putative morphological signatures in Kronichthys. Phylogenetic and species delimitation results clearly show the presence of four genetic lineages, three within Kronichthys heylandi along the coast from Rio de Janeiro to southern São Paulo and a single lineage encompassing both the nominal species Kronichthys lacerta and Kronichthys subteres from the Ribeira de Iguape basin to Santa Catarina in southern Brazil. Nonetheless, morphological data show overlapped ranges in morphometrics and a definition of only two morphotypes, with clear phenotypic differences in the teeth number: K. heylandi differs from K. subteres + K. lacerta by the higher number of premaxillary teeth (30–52 vs. 19–28) and higher number of dentary teeth (28–54 vs. 17–28). Headwater captures and connections of paleodrainages because of sea-level fluctuations represent the two major biogeographic processes promoting species diversification and lineage dispersal of Kronichthys in the Atlantic coastal range of Brazil.     

Molecular phylogeny of the subterranean genus Niphargus (Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids

The subterranean genus Niphargus is one of the most species‐rich genera among freshwater amphipods in the world, distributed in the Western Palearctic. Thus far, taxonomic and phylogenetic research has focused mainly on the European half of the genus range. In this study, 25 populations of Niphargus from Iran, Lebanon and the Crimean Peninsula were investigated. Bayesian inference based on 28S, H3 and COI gene sequences suggests that populations from the area belong to four different clades. Three species from Crimea and one species from Iran are nested at basal nodes, indicating their rather ancient origin. The rest of the species are younger and belong to two separate clades. One Crimean species is a sister‐species to east Romanian species. The second clade includes one species from Lebanon and all but one population from Iran. The origin of this clade corresponds to marine transgression between the Black Sea and Mediterranean approximately 12 Mya. This clade was further investigated taxonomically. Revision of qualitative morphological traits and unilocus species delimitation methods using COI suggest that this clade comprises 12–16 species, of which only three have been described so far. Multilocus coalescence delimitation methods (using fragments of COI, 28S, H3 and ITS) strongly supported 11 of these species. The remaining populations comprise at least two species complexes that require further and more detailed taxonomic research. © 2015 The Linnean Society of London     

Phylogenetic relationships in brown argus butterflies (Lepidoptera: Lycaenidae: Aricia) from northwestern Europe

Lycaenid butterflies of the Aricia agestisartaxerxes complex pose an unresolved taxonomic and conservation problem in northwestern Europe. Two key issues require resolution: (i) how many species of Aricia occur in northwestern Europe and what are their distributions?; (ii) how is the morphological variation observed in northwestern Europe best explained? We investigated phylogenetic relationships and phylogeographic patterns in this species group using mitochondrial and nuclear markers in comparison with morphological variation. A 325 bp fragment of the mitochondrial cytochromeb gene was sequenced from 179 individuals representing 18 populations from the UK and Scandinavia. Seventeen enzymecoding loci were analysed from 538 individuals from the same populations. Highly congruent phylogenies between mitochondrial and allozyme markers demonstrate that the sample is composed of two closely related species, A. agestis and A. artaxerxes. Both marker types also suggest that Scottish and northern Scandinavian A. artaxerxes populations are conspecific, and consequently do not support the endemic status of A. artaxerxes in the UK. The subspecies division of British populations of A. artaxerxes is also not supported by phylogenetic analyses. Allozyme and mitochondrial analyses cluster two populations from the Peak District, UK, differently. The former suggests that they are A. artaxerxes whilst the latter suggests they are A. agestis. Further research is required to find the reason for this disagreement, which could be associated with the different dynamics of nuclear and mitochondrial genes across a hybrid zone between the two species. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75 , 27–37.     

Integrative taxonomy of the primitively segmented spider genus Ganthela (Araneae: Mesothelae: Liphistiidae): DNA barcoding gap agrees with morphology

Species delimitation is difficult for taxa in which the morphological characters are poorly known because of the rarity of adult morphs or sexes, and in cryptic species. In primitively segmented spiders, family Liphistiidae, males are often unknown, and female genital morphology – usually species‐specific in spiders – exhibits considerable intraspecific variation. Here, we report on an integrative taxonomic study of the liphistiid genus Ganthela Xu & Kuntner, 2015, endemic to south‐east China, where males are only available for two of the seven morphological species (two known and five undescribed). We obtained DNA barcodes (cytochrome c oxidase subunit I gene, COI) for 51 newly collected specimens of six morphological species and analysed them using five species‐delimitation methods: DNA barcoding gap, species delimitation plugin [P ID(Liberal)], automatic barcode gap discovery (ABGD), generalized mixed Yule‐coalescent model (GMYC), and statistical parsimony (SP). Whereas the first three agreed with the morphology, GMYC and SP indicate several additional species. We used the consensus results to delimit and diagnose six Ganthela species, which in addition to the type species Ganthela yundingensis Xu, 2015, completes the revision of the genus. Although multi‐locus phylogenetic approaches may be needed for complex taxonomic delimitations, our results indicate that even single‐locus analyses based on the COI barcodes, if integrated with morphological and geographical data, may provide sufficiently reliable species delimitation. © 2015 The Linnean Society of London     

The genus Cyclops (Copepoda,Cyclopoida) in Europe

Although copepods of the genus Cyclops are among the most common and dominant plankton taxa of lakes in the northern temperate zone, their taxonomy is still unclear. We analysed an extensive array of Cyclops populations from Europe by means of molecular methods and evaluated morphological characters. Altogether, 68 populations of Cyclops species were sampled, assigned to morphospecies and sequenced for the 12S rRNA gene. Selected populations of each morphospecies were additionally sequenced for three mitochondrial (16S rRNA, cytochrome b, COI) and two nuclear genes (18S rRNA, ITS1) and analysed for micromorphological traits. Our analysis revealed fifteen lineages that can be regarded as separate species. Thirteen of these match currently accepted species, while the remaining two lineages were distinct from the other described species. Thus, their taxonomic status is open to further studies. Besides taxonomy, our study gives new insights into the ecology, distribution and phylogenetic relationships of these species. Finally, a set of morphological traits was selected to facilitate identification.     

In the foothill zone—Sabanejewia balcanica (Karaman 1922), in the lowland zone—Sabanejewia bulgarica (Drensky, 1928): Myth or reality?

The status of golden loaches (genus Sabanejewia) in the region of Central Europe and Balkans is still ambiguous. The greatest controversy is caused by species Sabanejewia balcanica and S. bulgarica. Both species are characterized by a wide spectrum of morphological variability and overlapping of distinguishing features, which then lead to difficulties in their determination. Previous phylogenetic studies aimed on the resolving of their taxonomic status did not include samples from their type localities and so led to a lack of their true distribution in this region. Therefore, the main aim of this study was to identify taxonomic status of golden loaches populations in the region of the middle Danube basin and adjacent areas on the model territory of Slovakia. For this purpose, we used novelty approach (morphological, molecular, and microhabitat) and we also included the missing samples from the type localities of both species. Based on mtDNA all the Slovakian samples reflected haplotype richness revealed on the type locality of S. bulgarica, although the genetic distances from other representatives of the genus Sabanejewia occurring are not significant. Within the morphology, we have revealed a great measure of variability in studied populations, which is largely caused by different habitat conditions and thus representing a phenotypic plasticity of these fish.     

Two new species of Acutogordius (Nematomorpha), with a brief review of literature data of this genus

We describe two new species of the nematomorph genus Acutogordius, A. sulawensis from Sulawesi and A. protectus from Madagascar. For comparative reasons, the other known species are briefly described and discussed. The genus Acutogordius now comprises nine species regarded as valid. They are distributed on the entire southern hemisphere, from South and Central America over Africa and South‐east Asia to Australia. The three male specimens of Acutogordius protectus differ in the shape of a cuticular structure, the postcloacal crescent, which has implications for the potential of this character as a taxonomic tool.     

Novel insights into the emergence of pathogens: the case of chestnut blight

Exotic, invasive pathogens have emerged repeatedly and continue to emerge to threaten the world’s forests. Ecosystem structure and function can be permanently changed when keystone tree species such as the American chestnut (Castanea dentata) are eliminated from a whole range by disease. The fungal ascomycete pathogen Cryphonectria parasitica is responsible for causing chestnut blight. Once the pathogen was introduced into the Eastern US, where chestnuts were predominant, chestnuts were all but eliminated. This pathogen is currently causing extensive damage in Europe. A study in this issue of Molecular Ecology sheds new light on the pattern and process of emergence of this devastating plant pathogen ( Dutech et al. 2012 ). The authors used microsatellite markers to investigate the evolutionary history of C. parasitica populations introduced into North America and Europe. To infer sources of migrants and the migration events, the authors included putative source populations endemic to China and Japan, inferred potentially unsampled populations and conducted a multivariate population genetic and complex ABC analysis. Cryphonectria parasitica emerges as an example of an introduced pathogen with limited genotypic diversity and some admixture in the invaded ranges, yet repeated invasions into different areas of Europe and the United States. This work sheds new light on the emergence of C. parasitica providing compelling evidence that this pathogen emerged by repeated migration and occasional admixture.     

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius)

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism‐level constraints. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 622–643.     

Phylogeny of European Pyrochroa (Coleoptera,Pyrochroidae) reveals cryptic taxa and different glacial histories

Only three saproxylic species of Pyrochroinae (Coleoptera: Pyrochroidae) are distributed in Europe, two of which belonging to Pyrochroa: P. coccinea and P. serraticornis. However, P. serraticornis is polytypic, for the presence of the endemic subspecies P. s. kiesenwetteri in southern Italy. Using both molecular and morphological data, we explored the phylogeny of the European Pyrochroa species. A multilocus (COI, CAD, 28S) phylogenetic analysis helped highlight different evolutionary histories for the two examined species. First, P. coccinea, distributed throughout Europe, showed a high differentiation among Italian and European populations. Furthermore, three different taxonomic entities were identified within P. serraticornis, among which the cryptic species Pyrochroa bifoveata sp. n. from central Europe is described and illustrated. A comprehensive identification key to the European Pyrochroinae is also provided. Our results also suggested an historical survival of P. coccinea and P. s. kiesenwetteri in glacial refugia in Italy, and a subsequent post-glacial spread of the former species throughout the Peninsula. In contrast, the current distribution of P. s. serraticornis likely originated from a post-glacial colonization of western European relict populations, while the survival of P. bifoveata plausibly occurred in more eastern glacial refugia (e.g. Carpathian or Balkan regions). Similarly, the European populations of P. coccinea could have originated from relict populations in glacial refugia out from the Italian Peninsula. More comprehensive data on the taxonomy, ecology and biogeography of Pyrochroa are needed to learn more about these species and to help preserve the European saproxylic fauna.     

Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South‐West Pacific)

The family Galatheidae is among the most diverse families of anomuran decapod crustaceans, and the South‐West Pacific is a biodiversity hot spot for these squat lobsters. Attempts to clarify the taxonomic and evolutionary relationships of the Galatheidae on the basis of morphological and molecular data have revealed the existence of several cryptic species, differentiated only by subtle morphological characters. Despite these efforts, however, relationships among genera are poorly understood, and the family is in need of a detailed systematic review. In this study, we assess material collected in different surveys conducted in the Solomon Islands, as well as comparative material from the Fiji Islands, by examining both the morphology of the specimens and two mitochondrial markers (cytochrome oxidase subunit I, COI, and 16S rRNA). These two sources of data revealed the existence of eight new species of squat lobster, four of which were ascribed to the genus Munida, two to the genus Paramunida, one to the genus Plesionida, and the last species was ascribed to the genus Agononida. These eight species are described along with phylogenetic relationships at the genus level. Our findings support the taxonomic status of the new species, yet the phylogenetic relationships are not yet fully resolved. Further molecular analysis of a larger data set of species, and more conserved genes, will help clarify the systematics of this group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 465–493.