A comparison of DNA-based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy

Species Delimitation Using Genomic Data: Options and Limitations

The most effective approaches for species discovery and species validation with genomic data remain underexplored. This study evaluates the merits and limitations of phylogenetic approaches based on the multispecies coalescent model and population genetic approaches for species discovery, i.e., species delimitation in the absence of prior knowledge, using genomic datasets from four well-known radiations. Furthermore, it demonstrates how geographic data can be integrated with the genomic data for species validation, i.e., for testing primary species hypotheses. The multispecies coalescent model-based approaches tr2 and soda resulted in high over-splitting of species, low percentages of species delimited according to the current classification, and low percentages of individuals assigned to the same species as in the current classification across all four species complexes studied. Conversely, the species numbers were slightly underestimated based on the structure results. Although the proportion of species delimited according to the current classification and the proportion of individuals assigned to the same species as in the current classification in the classifications based on the structure results is approximately twice that of the classifications proposed by the multispecies coalescent model-based approaches, it remains unsatisfactory. A slight over-splitting of species into population groups can be corrected by species validation with isolation-by-distance tests if a sufficient number of populations have been sampled for each species. Sampling design is an essential step in any taxonomic study, as it has a significant impact on the delimitation of the species and the possibility of their validation.

Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Pateranantahala (Gastropoda, Polygyridae)

Terrestrial gastropods are among the most imperiled groups of organisms on Earth. Many species have a complex taxonomic history, often including poorly defined subspecies, most of which have not been the focus of modern systematics research. Genomic tools, geometric morphometrics, and environmental niche modeling were used to assess the taxonomic status of Pateraclarkiinantahala (Clench & Banks, 1932), a subspecies of high conservation concern with a restricted range of approximately 3.3 km² in North Carolina, USA. A genome-scale dataset was generated that included individuals with morphologies matching P.c.nantahala, P.c.clarkii, and one individual with an intermediate form between P.c.nantahala and P.c.clarkii that was initially hypothesized as a potential hybrid. Mitochondrial phylogenetics, nuclear species tree inference, and phylogenetic networks were used to assess relationships and gene flow. Differences in shell shape via geometric morphometrics and whether the environmental niches of the two subspecies were significantly different were also examined. Molecular analyses indicated an absence of gene flow among lineages of P.clarkii sensu lato. Analyses rejected our hypothesis that the intermediate shelled form represented a hybrid, but instead indicated that it was a distinct lineage. Environmental niche models indicated significant differences in environmental niche between P.c.clarkii and P.c.nantahala, and geometric morphometrics indicated that P.c.nantahala had a significantly different shell shape. Given multiple lines of evidence, species-level recognition of P.nantahala is warranted.

Molecular phylogeny of the genus Chondrina (Gastropoda, Panpulmonata, Chondrinidae) in the Iberian Peninsula

Chondrina Reichenbach, 1828 is a highly diverse genus of terrestrial molluscs currently including 44 species with about 28 subspecific taxa. It is distributed through North Africa, central and southern Europe, from Portugal in the West to the Caucasus and Asia Minor in the East. Approximately 70% of the species are endemic to the Iberian Peninsula constituting its main center of speciation with 34 species. This genus includes many microendemic taxa, some of them not yet described, confined to limestone habitats (being strictly rock-dwelling species). They are distributed on rocky outcrops up to 2000 m.a.s.l. It is a genus of conical-fusiform snails that differ mainly in shell characters and in the number and position of teeth in their aperture. So far, molecular studies on Chondrina have been based exclusively on the mitochondrial Cytochrome Oxidase subunit I region (COI). These studies gave a first view of the phylogeny of the genus but many inner nodes were not statistically supported. The main objective of the study is to obtain a better understanding of the phylogeny and systematics of the genus Chondrina on the Iberian Peninsula, using multilocus molecular analysis. Partial sequences of the COI and 16S rRNA genes, as well as of the nuclear Internal Transcribed Spacer 1 (ITS1-5.8S) and Internal Transcribed Spacer 2 (5.8S-ITS2-28S) were obtained from individuals of all the extant Chondrina species known from the Iberian Peninsula. In addition to this, the newly obtained COI sequences were combined with those previously published in the GenBank. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods. The reconstructed phylogenies showed high values of support for more recent branches and basal nodes. Moreover, molecular species delimitation allowed to better definethe studied species and check the presence of new taxa.

Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete

Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3-9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.

One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data

Hemicycla mascaensis and H. diegoi are short-range endemics that occur allopatrically in small areas in the Teno Mountains in the western part of Tenerife (Canary Islands). Both taxa have been recognised as distinct species based on differences in shell morphology and genital anatomy. Preliminary molecular analyses using mitochondrial markers suggested a potential paraphyly of H. diegoi with regard to H. mascaensis. We here use multilocus AFLP data and ddRADseq data as well as distribution data, data on shell morphology and genital anatomy to assess the status of these taxa using phylogenetic analyses, species tree reconstruction and molecular species delimitation based on the multispecies coalescent as implemented in BFD* and BPP in an integrative approach. Our analyses show that, based on the analysis of multilocus data, the two taxa are reciprocally monophyletic. Species delimitation methods, however, tend to recognise all investigated populations as distinct species, albeit neither lending unambiguous support to any of the species hypotheses. The comparison of the anatomy of distal genital organs further suggests differentiation within H. mascaensis. This highlights the need for a balanced weighting of arguments from different lines of evidence to determine species status and calls for cautious interpretations of the results of molecular species delimitation analyses, especially in organisms with low active dispersal capacities and expected distinct population structuring such as land snails. Taking all available evidence into account, we favour to recognise H. mascaensis and H. diegoi as distinct species, acknowledging, though, that the recognition of both taxa as subspecies (with possibly a third yet undescribed) would also be an option as morphological differentiation is within the limits of other land snail species that are traditionally subdivided into subspecies.

Redescription of Monacha pantanellii (De Stefani, 1879), a species endemic to the central Apennines, Italy (Gastropoda, Eupulmonata, Hygromiidae) by an integrative molecular and morphological approach

Specimens obtained from ten populations of a Monacha species from the central Apennines were compared with six molecular lineages of Monacha cantiana s. l. (CAN-1, CAN-2, CAN-3, CAN-4, CAN-5, CAN-6) and two other Monacha species (M. cartusiana and M. parumcincta), treated as outgroup, by molecular (nucleotide sequences of two mitochondrial COI and 16S rDNA as well as two nuclear ITS2 and H3 gene fragments) and morphological (shell and genital anatomy) analysis. The results strongly suggest that these populations represent a separate species for which two names are available: the older Helix pantanellii De Stefani, 1879 and the junior M. ruffoi Giusti, 1973. The nucleotide sequences created well separated clades on each phylogenetic tree. Genital anatomy included several distinctive features concerning vaginal appendix, penis, penial papilla and flagellum; instead, shell characters only enabled them to be distinguished from M. cartusiana and M. parumcincta. Remarkably, populations of M. pantanellii show high morphological variability. Shell variability mainly concerns size, some populations having very small dimensions. Genital variability shows a more intricate pattern of all anatomical parts, being higher as regards the vagina and vaginal appendix. Despite this morphological variability, the K2P distance range of COI sequences between populations is narrow (0.2-4.5%), if we consider all but three of the 53 sequences obtained. This research confirmed that the species of Monacha and their molecularly distinguished lineages can only occasionally be recognised morphologically and that they have significant inter- and intra-population variability. The possibility of using an overall approach, including shell, genital and molecular evidence, was taken in order to establish a reliable taxonomic setting.

Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species

Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.

An integrative DNA barcoding framework of ladybird beetles (Coleoptera: Coccinellidae)

Even though ladybirds are well known as economically important biological control agents, an integrative framework of DNA barcoding research was not available for the family so far. We designed and present a set of efficient mini-barcoding primers to recover full DNA barcoding sequences for Coccinellidae, even for specimens collected 40 years ago. Based on these mini-barcoding primers, we obtained 104 full DNA barcode sequences for 104 species of Coccinellidae, in which 101 barcodes were newly reported for the first time. We also downloaded 870 COI barcode sequences (658 bp) from GenBank and BOLD database, belonging to 108 species within 46 genera, to assess the optimum genetic distance threshold and compare four methods of species delimitation (GMYC, bPTP, BIN and ABGD) to determine the most accurate approach for the family. The results suggested the existence of a 'barcode gap' and that 3% is likely an appropriate genetic distance threshold to delimit species of Coccinellidae using DNA barcodes. Species delimitation analyses confirm ABGD as an accurate and efficient approach, more suitable than the other three methods. Our research provides an integrative framework for DNA barcoding and descriptions of new taxa in Coccinellidae. Our results enrich DNA barcoding public reference libraries, including data for Chinese coccinellids. This will facilitate taxonomic identification and biodiversity monitoring of ladybirds using metabarcoding.

Living on the edge: comparative phylogeography and phylogenetics of Oreohelix land snails at their range edge in Western Canada

BACKGROUND

The biodiversity and distributions of terrestrial snails at local and regional scales are influenced by their low vagility and microhabitat specificity. The accessibility of large-bodied species and their characteristically high levels of genetic polymorphism make them excellent ecological and evolutionary models for studies on the phylogeography, phylogenetics, and conservation of organisms in fragmented populations. This study aims to elucidate the biodiversity, systematics, and distributions of genetic lineages within the genus Oreohelix at the northern and western periphery of their range.

RESULTS

We found four mitochondrial clades, three of which are putative subspecies of Oreohelix subrudis. One clade was geographically widespread, occurring within numerous sites in Cypress Hills and in the Rocky Mountains, a second was geographically restricted to the Rocky Mountains in Alberta, and a third was restricted to the Cypress Hills region. A fourth clade was the small-bodied species, O. cooperi. ITS2 sequence and screening data revealed three genetic clusters, of which one was O. cooperi. Cluster 1 contained most individuals in COI clade X and some from clade B and cluster 2 was predominantly made up of individuals from COI clades B and B' and a few from clade X. ITS2 alleles were shared in a narrow contact zone between two COI clades, suggestive of hybridization between the two.

CONCLUSIONS

A sky island known as Cypress Hills, in southeastern Alberta, Canada, is a biodiversity hotspot for terrestrial land snails in the genus Oreohelix. The observed phylogeographic patterns likely reflect reproductive isolation during the Last Glacial Maximum, followed by secondary contact due to passive, long-range dispersal resulting from low vagility, local adaptation, and complex glacial history.

DNA barcoding of aphid-associated ants (Hymenoptera, Formicidae) in a subtropical area of southern China

As one of the most abundant and complex groups of terrestrial insects, ants have associations with many other organismal groups, such as hemipteran insects producing honeydew. With the aim of expanding the knowledge base of ant species associated with aphids, this study analyzed mitochondrial COI barcodes of 301 ant samples for 37 aphid-associated ant species in a subtropical area of southern China. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zero to 7.7%% and 0.2 to 31.7%, respectively. Three barcoding approaches - Automatic Barcode Gap Discovery, Bayesian Poisson Tree Processes and Generalized Mixed Yule-coalescent - were used to help delimit ant species based on COI sequences, and their results corresponded well with most of the morphospecies. All three approaches indicate cryptic diversity may exist within Tetramorium bicarinatum and Technomyrmex albipes, with intraspecific genetic distances of 7.7% and 6.24%, respectively. Our analyses also reported five species for the first time from Fujian Province of China, and the COI sequences of nine species are newly added into the GenBank. This study provides information about species diversity of aphid-associated ants in subtropical China and compiles a DNA barcode reference library for future ant barcoding work.

Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups

Accurate species delimitation is crucial for studies of phylogeny, phylogeography, ecology, conservation and biogeography. The limits of species and genera in the Characidae family are controversial due to its uncertain phylogenetic relationships, high level of morphological homoplasy and the use of ambiguous morphological characters for descriptions. Here we establish species boundaries for Bryconamericus, Hemibrycon, Knodus and Eretmobrycon (Stevardiinae: Characidae), previously diagnosed with morphology, using three different barcoding approaches (GMYC, PTP, ABGD). Results revealed that species delimitation was successful by the use of a single-gene approach and by following a workflow in the context of integrative taxonomy, making evident problems and mistakes in the cataloging of Characidae species. Hence, it was possible to infer boundaries at genus level for clusters in the trees (GMYC and PTP) and automatic partitions (ABGD) which were consistent with some of recent taxonomic changes proposed in Characidae. We found that discordance cases between methods were linked to limitations of the methods and associated to putative species cluster closely related, some historically problematic in their diagnosis and identification. Furthermore, we suggested taxonomic changes and possibly new species, revealing a high degree of hidden diversity. Finally, we propose a workflow as a fast, accurate and objective way to delimit species from mitochondrial DNA sequences and to help clarify the classification of this group.

A taxonomic review and revisions of Microstomidae (Platyhelminthes: Macrostomorpha)

Microstomidae (Platyhelminthes: Macrostomorpha) diversity has been almost entirely ignored within recent years, likely due to inconsistent and often old taxonomic literature and a general rarity of sexually mature collected specimens. Herein, we reconstruct the phylogenetic relationships of the group using both previously published and new 18S and CO1 gene sequences. We present some taxonomic revisions of Microstomidae and further describe 8 new species of Microstomum based on both molecular and morphological evidence. Finally, we briefly review the morphological taxonomy of each species and provide a key to aid in future research and identification that is not dependent on reproductive morphology. Our goal is to clarify the taxonomy and facilitate future research into an otherwise very understudied group of tiny (but important) flatworms.

Exploration of phylogeography of Monachacantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae)

Two new lineages CAN-5 and CAN-6 were recognised in four populations of Monachacantiana (Montagu, 1803) s.l. from the Italian Apuan Alps by joint molecular and morphological analysis. They are different from other M.cantiana lineages known from English, Italian, Austrian and French populations, i.e. CAN-1, CAN-2, CAN-3 and CAN-4, as well as from the other Italian Monacha species used for comparisons (M.parumcincta and M.cartusiana). Although a definite taxonomic and nomenclatural setting seems to be premature, we suggest that the name or names for these new lineages as one or two species should be found among 19th century names (Helixsobara Mabille, 1881, H.ardesa Mabille, 1881, H.apuanica Mabille, 1881, H.carfaniensis De Stefani, 1883 and H.spallanzanii De Stefani, 1884).

Exploring Monacha cantiana (Montagu, 1803) phylogeography: cryptic lineages and new insights into the origin of the English populations (Eupulmonata, Stylommatophora, Hygromiidae)

Molecular analysis of nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) and 16S ribosomal DNA (16SrDNA) as well as nuclear histone 3 (H3) and internal transcribed spacer 2 of rDNA (ITS2) gene fragments together with morphological analysis of shell and genitalia features showed that English, French and Italian populations usually assigned to Monacha cantiana consist of four distinct lineages (CAN-1, CAN-2, CAN-3, CAN-4). One of these lineages (CAN-1) included most of the UK (five sites) and Italian (five sites) populations examined. Three other lineages represented populations from two sites in northern Italy (CAN-2), three sites in northern Italy and Austria (CAN-3), and two sites in south-eastern France (CAN-4). The taxonomic and nomenclatural setting is only currently available for lineages CAN-1 and CAN-4; a definitive frame for the other two requires much more research. The lineage CAN-1 corresponds to the true M. cantiana (Montagu, 1803) because it is the only one that includes topotypical English populations. The relationships and genetic distances support the hypothesis of the Italian origin of this lineage which was probably introduced to England by the Romans. The lineage CAN-4 is attributed to M. cemenelea (Risso, 1826), for which a neotype has been designated and deposited. Its diagnostic sequences of COI, 16SrDNA, H3 and ITS2 genes have also been deposited in GenBank. Molecular and morphological (shell and genitalia) features showed that M. parumcincta (Rossmässler, 1834) is a distinct taxon from the M. cantiana lineages.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].

Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia

In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.

At home at least: the taxonomic position of some north African Xerocrassa species (Pulmonata, )

In order to clarify the systematic position of Helix latastei Letourneux in Letourneux & Bourguignat, 1887, and Helix latasteopsis Letourneux & Bourguignat, 1887, a comprehensive approach using morphological and molecular methods is presented. The investigation of the genital organs of both species showed that they belong to the genus Xerocrassa Monterosato, 1892 with two very small dart sacs and a few tubiform glandulae mucosae. In our phylogenetic analysis using the mitochondrial markers COI, 16S and the nuclear cluster 5.8-ITS2-28S, the results of the anatomical research were confirmed. Thus, the genus Ereminella Pallary, 1919, which is based on H. latastei, becomes a junior synonym of Xerocrassa. A review of the genus-level taxa Xerobarcana Brandt, 1959, and Xeroregima Brandt, 1959, showed that these should also be considered as synonyms of Xerocrassa. A third species, Helix lacertara Bourguignat, 1863 from Algeria was found to be closely related to X. latastei based on its shell morphology. A map showing the distribution of the three species treated is supplied.

Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European Phoxinus (Cyprinidae)

BACKGROUND

Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used.

RESULTS

The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri, P. likai, and P. apollonicus. For three species (P. strandjae, P. strymonicus, P. morella), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus, were supported as secondary species hypotheses. Finally, six of the primary species hypotheses (P. phoxinus, P. lumaireul, P. karsticus, P. septimanae, P. marsilii and P. csikii) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis.

CONCLUSION

The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.

Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China

DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.

Integrative Profiling of Bee Communities from Habitats of Tropical Southern Yunnan (China)

Understanding and managing pollination service is hindered by taxonomic impediments and paucity of data, particularly in the tropics. Herein we apply integrative species delineation and taxonomy to test impacts of land use on the diversity of bee communities within Xishuangbanna (Yunnan, south China), a highly biodiverse tropical region which has undergone extensive land conversion to rubber plantation. 128 Operational Taxonomic Units (OTU) were inferred by an iterative and integrative approach. Bee activity differed significantly across land use samples, although community composition corresponded more to level of vegetation density, when accounting for spatial structure. Species diversity was high in young rubber plantations, although composition overlapped with other species-rich habitats (natural forest edge and river banks), and older plantations (>8 years) showed very low diversity under all measures. Community structures were similar between the natural forest interior and edge, although analysis indicated contrasting drivers of diversity, with clustering in the interior and overdispersion in the forest edge. Further, phylogenetic diversity and derived indices were underestimated when reference data were omitted from analysis. The description of bee communities herein permits more informed choices in land management with respect to ensuring continuation of essential services by bees.

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

Ongoing Speciation and Gene Flow between Taxonomically Challenging Trochulus Species Complex (Gastropoda: Hygromiidae)

Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy. We used an integrated approach based on morphological features, ecological preferences and two molecular markers: mitochondrial COI sequences and microsatellites. Comparison of these results demonstrated: (i) conchological distinction of T. striolatus and T. sericeus; (ii) anatomical, ecological and genetic differentiation of T. graminicola and (iii) concordance between morphological characters and mtDNA markers in T. striolatus. Moreover, our data showed an intricate evolutionary history within the genus Trochulus, which can be best explained by: (i) recent or ongoing gene flow between taxa or (ii) their large ancestral polymorphism. Both of these hypotheses suggest that diversification within this group of snails has occurred relatively recently. The mismatches between species defined on morphology and on molecular genetics indicate the complexity of the processes involved in the diversification of this genus.

The D3-D5 region of large subunit ribosomal DNA provides good resolution of German limnic and terrestrial nematode communities

Reliable and well-developed DNA barcode databases are indispensable for the identification of microscopic life. However, effectiveness of molecular barcoding in identifying terrestrial specimens, and nematodes in particular, has received little attention. In this study, ca 600 ribosomal large subunit DNA fragments (D3-D5 region) were successfully amplified for 79 limnic and terrestrial nematode species sampled at 147 locations across Germany. Distinctive DNA motifs in the LSU region were identified in 80% of all species examined. For 13 supposedly single morphospecies, 2-7 LSU barcode groups were detected with a wide range of intraspecific variations (0.09-7.9%). This region seems to be more suitable for the assessment of limno-terrestrial nematode diversity than the frequently used mitochondrial gene COI, as amplification success of the latter fragment is low for several nematode species. Our reference database for nematodes may serve as a starting point for applied and fundamental studies for these ubiquitous, ecologically highly relevant, organisms.

Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)

Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.

Molecular phylogeny and a modified approach of character-based barcoding refining the taxonomy of New Caledonian freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae)

The islands of New Caledonia represent one of the world's biodiversity hotspots with many endemic species including freshwater gastropods of the family Tateidae. A phylogenetic analysis based on the mitochondrial COI and 16S rRNA and the nuclear ITS2 genes revealed two cryptic genera, Crosseana gen. n. and Novacaledonia gen. n. In order to provide character-based diagnoses we modified a DNA barcoding approach identifying strings of pairwise diagnostic characters, i.e. alignment positions, at which two genera are alternatively fixed for different nucleotides. The combination or string of all pairwise diagnostic characters was unique for each genus. Inconsistent mitochondrial and nuclear topologies suggest that Hemistomia cockerelli Haase and Bouchet, 1998 and H. fabrorum Haase and Bouchet, 1998, two morphologically well-defined species, hybridize. The age of the most recent common ancestor of the New Caledonian radiation of Tateidae was estimated at 24.6±9.5 MY. These findings are in line with the notion that New Caledonia is rather a Darwinian island that was colonized after an extended phase of submergence - in case of the tateids probably from Australia - despite being a fragment of Gondwanaland.

Delineating species with DNA barcodes: a case of taxon dependent method performance in moths

The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.