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Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo‐West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological‐scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation. [ABSTRACT FROM AUTHOR]

The simple thalloid liverwort Apopellia endiviifolia is a widespread Holarctic species belonging to the family Pelliaceae. European populations of this species comprise two distinct evolutionary lineages named “species A”, known also as water form, and typical, mainly terrestrial forms named “species B”. Newly sequenced, assembled and annotated chloroplast genomes of six European specimens belonging to the two cryptic lineages occupying different microhabitats, revealed the structure typical for liverworts and previously sequenced reference. The plastomes of A. endiviifolia are 120,537–120,947 bp long with a structure typical for most plants, including a pair of IR regions (each of 9,092–9,207 bp) separated by LSC (82,506–82,609 bp) and SSC (19,854–19,924 bp) regions and consist of 121 unique genes, including 81 protein-coding genes, 6 genes of unknown function (ycf genes), 4 ribosomal RNAs and 30 transfer RNAs. Comparative analysis of typical, terrestrial and water forms revealed 4971 molecular diagnostic characters (MDCs), which exceeds numbers found in many well recognized liverworts taxa. Moreover, beside the presence of evolutionary hotspots like ycf1 and ycf2 genes and several intergenic spacer like ndhB-psbM, rps4-ndhJ and ndhC-atpE, the molecular identification of Apopellia cryptic species was possible by almost 98% of 500 bp long frames simulating mini barcodes. The different ecological niches can be driven by different pressures of positive selection, which was detected in nine genes including ccsA, ndhD, ndhF, petA, psbB, psbC, rpoB, ycf1 and ycf2. Despite clearly genetic differences and ecological preferences, the current observation of morphological differentiation does not no allow to separate terrestrial and water forms into taxonomic species.

Abstract Background Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as “cryptic species”. Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. Results Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61–2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. Conclusions Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai–Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.

Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther‐smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant–pathogen pairs of anther‐smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC‐RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host–pathogen pairs contribute to a better understanding of co‐evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce. [ABSTRACT FROM AUTHOR]

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south‐western and south‐eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south‐western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south‐eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150‐km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2–27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population‐level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation. [ABSTRACT FROM AUTHOR]

Pteropyrum is a small genus of Polygonaceae with four species from the arid regions of Iran and adjacent countries. Pteropyrum spp. are not precisely delimitated and are difficult to identify because of their high plasticity in morphological characters. Pteropyrum (C3) has a close affinity to Calligonum (C4) and is therefore a suitable case for C4 evolutionary studies. We investigated the morphology and micromorphology (including pollen morphology) of Pteropyrum and elucidated the phylogenetic relationships with Atraphaxis and Calligonum using nuclear ITS sequences. Characteristics of the photosynthetic tissues such as volume and number of layers of primary carbon assimilation tissues (PCA) and photosynthetic carbon reduction tissue (PCR) were studied. In addition, the leaf and cotyledon anatomical characters of Pteropyrum (C3), Atraphaxis (C3) and Calligonum (C4), and their δ 13C values were compared to look for evolutionary changes in assimilating organs. The molecular phylogenetic tree identifies two strongly supported clades in Pteropyrum and its close relationship with Calligonum , confirming previous studies. Some morphologically similar species belong to different clades, which is probably due to convergent evolution and homoplasy. Leaf anatomical studies show that Atraphaxis has a multilayered mesophyll tissue, whereas Calligonum has one-layered mesophyll cells. The volume and layer number of mesophyll tissue cells decreases, whereas water storage tissue area significantly increases from Atraphaxis to Pteropyrum and Calligonum. This phenomenon confirms previous studies in other lineages with C4 salsoloid anatomy that have evolved through increasing of water storage tissue and succulence of assimilating organs. In the taxonomic part of the paper, a key to identification of accepted taxa of Pteropyrum , description of species and distribution maps are presented based on numerous herbarium specimens and our own rich collections from the field. Four new species are described based on a combination of morphology of seedlings and mature plants, pollen morphology and molecular data. A subspecific classification is suggested to show morpho-geographical variation of Pteropyrum aucheri s.l. [ABSTRACT FROM AUTHOR]

Pteropyrum is a small genus of Polygonaceae with four species from the arid regions of Iran and adjacent countries. Pteropyrum spp. are not precisely delimitated and are difficult to identify because of their high plasticity in morphological characters. Pteropyrum (C3) has a close affinity to Calligonum (C4) and is therefore a suitable case for C4 evolutionary studies. We investigated the morphology and micromorphology (including pollen morphology) of Pteropyrum and elucidated the phylogenetic relationships with Atraphaxis and Calligonum using nuclear ITS sequences. Characteristics of the photosynthetic tissues such as volume and number of layers of primary carbon assimilation tissues (PCA) and photosynthetic carbon reduction tissue (PCR) were studied. In addition, the leaf and cotyledon anatomical characters of Pteropyrum (C3), Atraphaxis (C3) and Calligonum (C4), and their δ 13C values were compared to look for evolutionary changes in assimilating organs. The molecular phylogenetic tree identifies two strongly supported clades in Pteropyrum and its close relationship with Calligonum , confirming previous studies. Some morphologically similar species belong to different clades, which is probably due to convergent evolution and homoplasy. Leaf anatomical studies show that Atraphaxis has a multilayered mesophyll tissue, whereas Calligonum has one-layered mesophyll cells. The volume and layer number of mesophyll tissue cells decreases, whereas water storage tissue area significantly increases from Atraphaxis to Pteropyrum and Calligonum. This phenomenon confirms previous studies in other lineages with C4 salsoloid anatomy that have evolved through increasing of water storage tissue and succulence of assimilating organs. In the taxonomic part of the paper, a key to identification of accepted taxa of Pteropyrum , description of species and distribution maps are presented based on numerous herbarium specimens and our own rich collections from the field. Four new species are described based on a combination of morphology of seedlings and mature plants, pollen morphology and molecular data. A subspecific classification is suggested to show morpho-geographical variation of Pteropyrum aucheri s.l. [ABSTRACT FROM AUTHOR]

The diversity of bats worldwide includes large numbers of cryptic species, partly because divergence in acoustic traits such as echolocation calls are under stronger selection than differences in visual appearance in these nocturnal mammals. Island faunas often contain disproportionate numbers of endemic species, and hence we might expect cryptic, endemic species to be discovered relatively frequently in bats inhabiting islands. Species are best defined when multiple lines of evidence supports their diagnosis. Here we use morphometric, acoustic, and molecular phylogenetic data to show that a horseshoe bat in the Andaman Islands is distinct in all three aspects, supporting its status as a distinct species. We recommend investigation into possible new and endemic bat species on islands by using integrated approaches that provide independent lines of evidence for taxonomic distinctiveness. We provide a formal redescription of the taxon newly raised to species level, Rhinolophus andamanensis Dobson, 1872. [ABSTRACT FROM AUTHOR]

(A) Distribution of sampling localities. (B) Results of the Structure analysis based on the SNPs at K = 2. (C) Principal components analysis (PCA) of 12,548 SNPs obtained from P. armandii and its relatives. (D) Phylogenetic analysis Maximum-likelihood tree constructed from the 13,906 SNPs identified in P. armandii. (E) Heat maps for the net genetic distances (Da) between different groups or species. (F) Predicted distributions of the northern and southern subdivisions using Maxent. • Cryptic speciation has occurred in Pinus armandii. • The interactions of geography and ecology led to the speciation. • Both geography and ecology contributed to the high conifer diversity in HHM. Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii , an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains. [ABSTRACT FROM AUTHOR]

The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide, from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rRNA gene phylogenies, unlike most previous analyses based on two sequences. [ABSTRACT FROM AUTHOR]

Bemisia tabaci (the tobacco whitefly) is an important agricultural pest of global significance primarily because of its ability to transmit multiple damaging plant viruses. To date, UK outbreaks of the whitefly have been restricted to glasshouses and there are no records of the whitefly establishing outdoors during the summer. This is despite the fact that annual degree-day models (that estimate accumulated warmth over the year above the development threshold), indicate that B. tabaci has the thermal potential for multiple summer generations in the UK. A set of 49 climate indices calculated using the present day climate (1986–2015) were therefore compared between the UK and the south of France, where B. tabaci is able to establish outdoors, to identify the factors limiting its establishment. The number of cold days and nights in summer, as well as the time spent within the whitefly’s optimum temperature range, were most significantly different between the two areas. These indices may impact the development of B. tabaci and offer an explanation for the absence of the whitefly outdoors in the UK during the summer. Further analyses undertaken with climate projections suggest that in a 2–4°C warmer world this pest could pose a risk to outdoor UK crops in July and August. A clear south-north gradient can be demonstrated for these indices. Linking any possible northwards spread of B. tabaci populations outdoors in France with changes in these indices could therefore provide an important indicator of any change in the risks of outdoor populations of this species developing in the UK. The effectiveness of climate indices in pest risk analysis is compellingly demonstrated, and it is recommended that in-depth comparisons of climatic indices between areas of pest presence and absence are conducted in other situations where forecasting the risks of pest establishment are complex and challenging. [ABSTRACT FROM AUTHOR]

The bonnethead shark, Sphyrna tiburo, is a small elasmobranch distributed in the Eastern Pacific from southern California to Ecuador, and along the Western Atlantic, with preferences for continental margins of North, Central and South America, the Gulf of Mexico, and the Caribbean. Recent studies have suggested that it could be under a process of cryptic speciation, with the possibility to find different species in similar geographic locations. Here we assessed the population structure and genetic diversity of this highly philopatric and non-dispersive species in the Bocas del Toro Archipelago, Panama. Fragments of the mitochondrial genes cytochrome oxidase I and control region, were used to test the genetic structure of adult and juvenile S. tiburo in this area, and were compared with other locations of the Western Atlantic and Belize. We found significant genetic differentiation between Caribbean bonnethead sharks from Bocas del Toro and Belize, when compared to bonnetheads from other locations of the Western Atlantic. These results also suggest that Bocas del Toro could constitute a different genetic population unit for this species, whereby bonnethead sharks in this area could belong to a unique stock. The information obtained in this study could improve our understanding of the population dynamics of the bonnethead shark throughout its distribution range, and may be used as a baseline for future conservation initiatives for coastal sharks in Central America, a poorly studied an often overlooked region for shark conservation and research. [ABSTRACT FROM AUTHOR]

Our understanding of the flora of China has greatly improved during the last 100 years but effective management of the rich biodiversity and unique natural resources requires resolving the taxonomic limitations of existing treatments. Here, we focus on the epiphytic genus Scleroglossum with special emphasis on the occurrences in Hainan and Yunnan of mainland China. By combining fieldwork, herbarium studies, and DNA barcoding we test the hypothesis that this genus is represented by more than one species in China. Our integrative results show the Yunnan accessions are distinct from those in Hainan in both phenotypic and genotypic variation. The Yunnan accessions belong to S. pusillum, whereas the Hainan accessions represent a distinct species displaying the morphological characteristics of S. sulcatum. Genotypic evidence suggests the occurrence of cryptic diversity among accessions with the morphology of S. sulcatum. In summary, the study contributes to the crucial assessment of the plant diversity in Yunnan and illustrates the importance of integrating collection efforts and DNA barcoding approaches to enable effective assessment of the epiphytic diversity of Yunnan. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The nucleotide sequences of two mitochondrial genes (16S rDNA and COI) were compared among all species of Hediste, including five nominal and two cryptic species (H. atoka and H. diversicolor both consisting of two cryptic species, H. diadroma, H. japonica, and H. limnicola), as well as a newly found undescribed species (H. sp.), to estimate their phylogenetic relationships. The analysis using 16S rDNA sequence supported the monophyly of all five nominal species and H. sp., with no detection of the genetic differentiation between the two cryptic species in both H. atoka and H. diversicolor. However, analysis using COI sequence detected a marked differentiation between the cryptic species, and indicated that the two forms of H. atoka were separated into distinct clades; form A was included in a clade together with H. diversicolor, H. limnicola, and H. sp., whereas form B was included in another clade together with H. diadroma. Based on the topology of our phylogenetic analysis using the combined data set of 16S rDNA and COI, a hypothesis on the evolutionary history of the worldwide speciation in Hediste is proposed. This hypothesis seems to correspond well with the geographical distributions of current species and their morphological differentiation, supporting the previous hypothesis that the unique epitokous swarming and planktic larval development evolved independently in H. diadroma and H. japonica in eastern Asia. We also show that no or few interspecific substitutions have occurred in sequences of nuclear DNA (18S rDNA, 28S rDNA, and histone H3) in Hediste. [ABSTRACT FROM AUTHOR]

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected. [ABSTRACT FROM AUTHOR]

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0–5.3% while congeneric distances varied from 2.8–23.2%. Excepting one species pair (Oxyopes azhari–Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries. [ABSTRACT FROM AUTHOR]

Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns. [ABSTRACT FROM AUTHOR]

Species from the genus Paralipsis are obligatory endoparasitoids of root aphids in the Palaearctic. It is known that these species are broadly distributed, parasitizing various aphid hosts and showing great biological and ecological diversity. On the other hand, this group of endoparasitoids is understudied and was thought to be represented by a single species in Europe, viz., Paralipsis enervis (Nees). However, recent description of two new species indicated the possibility of cryptic speciation and recognition of additional Paralipsis species in Europe. In this research, Paralipsis specimens collected during the last 60 years from eight European countries, as well as one sample from Morocco, were subjected to molecular and morphological characterization. Newly designed genus-specific degenerative primers successfully targeted short overlapping fragments of COI of the mitochondrial DNA. Molecular analyses showed clear separation of four independent lineages, two of which are the known species P. enervis and P. tibiator, while two new species are described here, viz., P. brachycaudi Tomanović & Starý, sp. n. and P. rugosa Tomanović & Starý, sp. n. No clear specialization of the taxa to a strict root aphid host has been determined. The recognized mitochondrial lineages were distinct one from another, but with a substantial within-lineage divergence rate, clearly indicating the complexity of this group of parasitoids, on which further research is required in order to clarify the factors triggering their genetic differentiation. We reviewed literature data and new records of Paralipsis enervis aphid host associations and distributions. A key for the identification of all known Paralipsis species is provided and illustrated. [ABSTRACT FROM AUTHOR]

The distribution of the Southern Ocean (SO) biota is the result of major geological, oceanographic, and climate changes during the last 50 million years (Ma). Several groups of marine benthic organisms exhibit marked taxonomic similarities between the Antarctic Peninsula and southern South America, where families, genera, and even species are currently co-distributed in these continents. Several species of macroalgae including Gigartina skottsbergii, Plocamium cartilagineum, and Iridaea cordata are currently found on both sides of the Drake Passage. Advances in molecular techniques have allowed estimating phylogenetic relationships, levels of differentiation and divergence time estimates between populations from these continents in order to determine whether they constitute separate evolutionary units. In this study, we determine whether Iridaea cordata represents the same evolutionary unit in southern South America and the Antarctic Peninsula or if populations on the two sides of the Drake Passage represent different genetic lineages. According to our results, I. cordata populations from the Antarctic Peninsula and South America are clearly distinguishable evolutionary units with 8.31% and 3.17% mtDNA and cpDNA molecular divergence, respectively. The separation between Antarctic and South American populations of I. cordata occurred at the end of the Miocene, between 5 Ma (rbcL) and 9 Ma (COI-5P). These results are similar to those reported in G. skottsbergii on both sides of the Drake Passage. Thus, I. cordata populations on the two sides of the Drake Passage should be considered two sister species. Cryptic speciation plays an important role in the evolution of the Southern Ocean; thus, the systematics, biogeography, and biodiversity of the region require major revisions. [ABSTRACT FROM AUTHOR]

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

Most research on extant planktonic foraminifera has been directed towards larger species (>0.150 mm) which can be easily manipulated, counted and yield enough calcite for geochemical analyses. This has drawn attention towards the macroperforate clade and created an impression of their numerical and ecological dominance. Drawing such conclusions from the study of such "giants" is a dangerous path. There were times in the evolutionary history of planktonic foraminifera when all species were smaller than 0.1 mm and indeed numerous small taxa, mainly from the microperforate clade, have been formally described from the modern plankton. The significance of these small, obscure and neglected species is poorly characterized and their relationship to the newly discovered hyperabundant but uncharacterized lineages of planktonic foraminifera in metabarcoding datasets is unknown. To determine, who is hiding in the metabarcoding datasets, we carried out an extensive sequencing of 18S rDNA targeted at small and obscure species. The sequences of the newly characterized small and obscure taxa match many of the previously uncharacterized lineages found in metabarcoding data. This indicates that most of the modern diversity in planktonic foraminifera has been taxonomically captured, but the role of the small and neglected taxa has been severely underestimated. [ABSTRACT FROM AUTHOR]

Bemisia tabaci is one of the most threatening pests in agriculture, causing significant losses to many important crops on a global scale. The dramatic increase and availability of sequence data for B. tabaci species complex and its bacterial endosymbionts is critical for developing emerging sustainable pest management strategies which are based on pinpointing the global diversity of this important pest and its bacterial endosymbionts. To unravel the global genetic diversity of B. tabaci species complex focusing on its associated endosymbionts, along with Israeli whitefly populations collected in this study, we combined available sequences in databases, resulting in a total of 4,253 mitochondrial cytochrome oxidase I (mtCOI) sequences from 82 countries and 1,226 16S/23S rRNA endosymbiont sequences from 32 countries that were analyzed. Using Bayesian phylogenetic analysis, we identified two new B. tabaci groups within the species complex and described the global distribution of endosymbionts within this complex. Our analyses revealed complex divergence of the different endosymbiont sequences within the species complex, with overall one Hamiltonella, two Porteria (P1 and P2), two Arsenophonus (A1 and A2), two Wolbachia (super-groups O and B), four Cardinium (C1-C4) and three Rickettsia (R1-R3) groups were identified. Our comprehensive analysis provides an updated important resource for this globally important pest and its secondary symbionts, which have been a major subject for research in last three decades. [ABSTRACT FROM AUTHOR]

The coastal tailed frog (Ascaphus truei) is endemic to the Pacific Northwest of North America and is listed as a species of Special Concern under the Canadian Species at Risk Act. Its range is limited to British Columbia where it occurs widely west of the Coast Mountain Ranges extending north almost to the Alaskan Panhandle. The present study focused on surveying within the Cayoosh, Bridge (Shulaps), Seton, Anderson, Carpenter, and Downton Lake drainages. Four years of previous inventory efforts using conventional time-constrained search (TCS) methods detected tailed frog at 23/292 discrete sites (7.9% detection rate) in seven watersheds. Non-invasive environmental DNA (eDNA) methods hold promise for cryptic and low-abundance species detection. We rigorously validated a quantitative real-time polymerase chain reaction (qPCR)-based tool for detecting coastal tailed frog eDNA in water samples. This eASTR4 test is highly specific and sensitive. We applied a two-step targeted eDNA analysis approach on duplicate filtered water samples from a total of 72 sites collected over five days. The first IntegritE-DNA step mitigates false negative results and tests all DNA samples for the ability to support amplification from endogenous plant chloroplast DNA as a measure of sample viability. Three DNA samples failed this step even after inhibitor clean up suggesting that these samples were poor quality and not reliable for targeted species’ DNA analyses. All other DNA samples were deemed viable and were then tested for species-specific DNA. Coastal tailed frog eDNA was detected in 55/72 (76%) discrete stream reaches; nine sites with historical known occurrence were all eDNA positive. The false negative rate for TCS compared to eDNA methods was 58%. The results expand known coastal tailed frog distribution to 24 watersheds effectively more than tripling extant occurrences and confirm a previously suspected, apparently isolated coastal tailed frog metapopulation in the Shulaps drainage. [ABSTRACT FROM AUTHOR]

The genus Polymixia is the only survivor of a Late Cretaceous marine fish radiation and is often said to be the most primitive living acanthomorph (i.e., Polymixia possesses the greatest number of primitive character states for Acanthomorpha). Recent studies, including this one, place Polymixia as the sister to all other Paracanthopterygii. Despite its importance, most species of Polymixia are extremely difficult to discriminate on the basis of morphology. As a result, the number of valid species is uncertain. Moreover, there has never been a phylogenetic analysis of the genus. Thus, a molecular phylogenetic study was needed to clarify species boundaries and to resolve relationships within the genus. Tissue or DNA samples backed by museum vouchers were obtained for most species, with additional samples from new geographic areas representing specimens with distinctively different meristics and uncertain identifications. Seven loci (five nuclear and two mitochondrial) were sequenced, from which Bayesian and maximum-likelihood trees were generated. Results reveal nine species-level clades, of which five represent previously known species (Polymixia berndti, P. japonica, P. longispina, P. lowei, and P. nobilis). Surprisingly, results also reveal four previously unknown species-level clades, one close to P. lowei, one close to P. nobilis, and two new species clades related to P. japonica. The species clades are distinguished by their phylogenetic histories, sequence differences, geographic distributions, and morphologies. The clade containing P. berndti is recovered as the sister to all other species of Polymixia. Its genetic variability suggests that it might contain two or more species and it is referred to here as a “species complex”. Polymixia nobilis, the type species, was previously thought to be restricted to the Atlantic, but is now shown to be widespread in the Pacific and possibly in the Indian Ocean. Specimens from waters off Australia identified as P. busakhini actually belong to P. nobilis. In contrast, P. japonica is confirmed only in the area near Japan and the East China Sea; other more distant records are misidentifications. Wide (antipodal) geographic distributions are seen in several clades, including P. nobilis, the P. berndti species complex, and the P. japonica species group. The new phylogeny helps explain the evolution of some morphological characters previously used to distinguish groups of species, particularly dorsal-fin soft-ray count, shape of rows of scale ctenii, and number of pyloric caeca. [ABSTRACT FROM AUTHOR]

The use of subtle features as species diagnostic traits in taxa with high morphological similarity sometimes fails in discriminating intraspecific variation from interspecific differences, leading to an incorrect species delimitation. A clear assessment of species boundaries is particularly relevant in disease vector organisms in order to understand epidemiological and evolutionary processes that affect transmission capacity. Here, we assess the validity of the recently described Rhodnius taquarussuensis (da Rosa et al., 2017) using interspecific crosses and molecular markers. We did not detect differences in hatching rates in interspecific crosses between R. taquarussuensis and R. neglectus (Lent, 1954). Furthermore, genetic divergence and species delimitation analyses show that R. taquarussuensis is not an independent lineage in the R. prolixus group. These results suggest that R. taquarussuensis is a phenotypic form of R. neglectus instead of a distinct species. We would like to stress that different sources of evidence are needed to correctly delimit species. We consider this is an important step in understanding vectorial Chagas disease spread and transmission. [ABSTRACT FROM AUTHOR]

Taxonomy of Geastrum species in the neotropics has been subject to divergent opinions among specialists. In our study, type collections were reassessed and compared with recent collections in order to delimit species in Geastrum, sect. Myceliostroma, subsect. Epigaea. A thorough review of morphologic features combined with barcode and phylogenetic analyses (ITS and LSU nrDNA) revealed six new species (G. neoamericanum, G. rubellum, G. brunneocapillatum, G. baculicrystallum, G. rubropusillum and G. courtecuissei). In additon, the presence of hairs on the exoperidium, a commonly used feature to diagnose Geastrum species, proved to be ineffective because it is a derived character within subsect. Epigaea. [ABSTRACT FROM AUTHOR]

Understanding natural variations in the life history traits of reef-building corals under different environmental conditions is an area of active research. This study compares variability in the reproductive and genetic traits of the hermaphroditic broadcast spawning coral Acropora hyacinthus, from the Western Pacific Region, across six different latitudes [Japan (33° and 31°N), Taiwan (23°, 22° and 21°N), and Indonesia (5°S)]. Egg sizes among corals in the lowest latitude studied were significantly larger than those at high latitudes, while the mean number of eggs were significantly different only among high latitude and two out of the three mid latitude locations studied. Egg numbers were significantly negatively correlated with egg and testis volumes, indicating reproductive trade-offs across locations. Female gonad volumes were smaller at high latitudes but significantly larger at lower latitudes, being positively correlated with seawater temperatures. Furthermore, high genetic similarities among populations suggest active gene flow among low-, mid- and high-latitude locations. An exception to this trend, the mid-latitude location of Penghu (off western Taiwan) formed an independent group with highly similar genetic and reproductive traits, suggesting reproductive isolation with local adaptations. This study reports natural spatial variations in the reproductive traits of A. hyacinthus at different latitudinal locations, which may serve as baseline information to predict how the life histories of corals in general respond to the impacts of climate change. [ABSTRACT FROM AUTHOR]

Acoustic signals play an important role in premating isolation based on sexual selection within many taxa. Many male parasitic wasps produce characteristic courtship songs used by females in mate selection. In Cotesia (Hymenoptera: Braconidae: Microgastrinae), courtship songs are generated by wing fanning with repetitive pulses in stereotypical patterns. Our objectives were to sample the diversity of courtship songs within Cotesia and to identify e underlying patterns of differentiation. We compared songs among 12 of ca. 80 Cotesia species in North America, including ten species that have not been recorded previously. For Cotesia congregata, we compared songs of wasps originating from six different host-foodplant sources, two of which are considered incipient species. Songs of emergent males from wild caterpillar hosts in five different families were recorded, and pattern, frequency, and duration of song elements analyzed. Principal component analysis converted the seven elements characterized into four uncorrelated components used in a hierarchical cluster analysis and grouped species by similarity of song structure. Species songs varied significantly in duration of repeating pulse and buzz elements and/or in fundamental frequency. Cluster analysis resolved similar species groups in agreement with the most recent molecular phylogeny for Cotesia spp., indicating the potential for using courtship songs as a predictor of genetic relatedness. Courtship song analysis may aid in identifying closely related cryptic species that overlap spatially, and provide insight into the evolution of this highly diverse and agriculturally important taxon. [ABSTRACT FROM AUTHOR]

White-eyes (Zosterops spp.) are a group of small passerines distributed across the Eastern Hemisphere that have become a textbook example of rapid speciation. However, traditional taxonomy has relied heavily on conservative plumage features to delimit white-eye species boundaries, resulting in several recent demonstrations of misclassification. Resolution of confused taxonomy is important in order to correctly delimit species and identify taxa which may require conservation, particularly in Asia where the songbird trade is decimating wild populations. In this study, we aim to untangle multiple instances of confused taxonomic treatment in three large, widespread Asian wastebasket species complexes of white-eye (Oriental White-eye Zosterops palpebrosus, Japanese White-eye Zosterops japonicus and Mountain White-eye Zosterops montanus) renowned for their conservative morphology. Using mitochondrial DNA from 173 individuals spanning 42 taxa, we uncovered extensive polyphyly in Z. palpebrosus and Z. japonicus and propose some radically revised species limits under which former members of Z. palpebrosus and Z. japonicus would be reassigned into four and two different species, respectively. The revised taxonomy results in a net loss of two previously recognized species and a net gain of two newly recognized species, leading to significant taxonomic change but a lack of additional species-level diversity. One of the newly elevated species, Zosterops melanurus from Java and Bali, is also the world's most heavily traded songbird and requires urgent conservation attention. [ABSTRACT FROM AUTHOR]

The species Loxosceles rufescens is native to the Mediterranean but considered cosmopolitan because it has been dispersed worldwide. A previous study revealed 11 evolutionary lineages across the Mediterranean, grouped into two main clades, without any clear phylogeographic pattern. The high genetic diversity within this species (p-distances of up to 7.8% in some Mediterranean lineages), together with the results obtained with different species delimitation methods (GMYC, TCS) could indicate the existence of cryptic species. Here we compare the mitochondrial and microsatellite diversity to elucidate if the lineages of L. rufescens in the Mediterranean should be considered different species (cryptic species) or populations of the same species. To do so, we analyzed the cox1 diversity of 196 individuals, of which, we genotyped 148, sampled from 19 localities across the Mediterranean. STRUCTURE analyses of microsatellite data identified two genetic clusters of L. rufescens. One cluster included individuals from Western Mediterranean localities (Iberian Peninsula, Morocco, Balearic Islands) and Israel, while the second one grouped individuals from Italian and Greek localities, including Sardinia, Sicily and Tunisia. These patterns suggest that geographic proximity is the more significant factor in the clustering with microsatellite data and shows the existence of gene flow between the nearest geographic areas, even if the individuals belong to different mitochondrial lineages or clades. The lack of correspondence between both genetic markers suggests that the evolutionary lineages found within L. rufescens should not be considered different species. We conclude that these phylogenetic linages and their distribution may be the result of the maternal evolutionary history of the species and human-mediated dispersion. [ABSTRACT FROM AUTHOR]

We provide the first detailed identification of Barents Sea cold seep frenulate hosts and their symbionts. Mitochondrial COI sequence analysis, in combination with detailed morphological investigations through both light and electron microscopy was used for identifying frenulate hosts, and comparing them to Oligobrachia haakonmosbiensis and Oligobrachia webbi, two morphologically similar species known from the Norwegian Sea. Specimens from sites previously assumed to host O. haakonmosbiensis were included in our molecular analysis, which allowed us to provide new insight on the debate regarding species identity of these Oligobrachia worms. Our results indicate that high Arctic seeps are inhabited by a species that though closely related to Oligobrachia haakonmosbiensis, is nonetheless distinct. We refer to this group as the Oligobrachia sp. CPL-clade, based on the colloquial names of the sites they are currently known to inhabit. Since members of the Oligobrachia sp. CPL-clade cannot be distinguished from O. haakonmosbiensis or O. webbi based on morphology, we suggest that a complex of cryptic Oligobrachia species inhabit seeps in the Norwegian Sea and the Arctic. The symbionts of the Oligobrachia sp. CPL-clade were also found to be closely related to O. haakonmosbiensis symbionts, but genetically distinct. Fluorescent in situ hybridization and transmission electron micrographs revealed extremely dense populations of bacteria within the trophosome of members of the Oligobrachia sp. CPL-clade, which is unusual for frenulates. Bacterial genes for sulfur oxidation were detected and small rod shaped bacteria (round in cross section), typical of siboglinid-associated sulfur-oxidizing bacteria, were seen on electron micrographs of trophosome bacteriocytes, suggesting that sulfide constitutes the main energy source. We hypothesize that specific, local geochemical conditions, in particular, high sulfide fluxes and concentrations could account for the unusually high symbiont densities in members of the Oligrobrachia sp. CPL-clade. [ABSTRACT FROM AUTHOR]

The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa. [ABSTRACT FROM AUTHOR]

Benthic foraminifera, and certainly symbiont-bearing (large) benthic foraminifera are generally considered to have large geographic ranges in combination with significant ecomorphological variation. With the advance of molecular phylogenetic approaches, supported or preceded by detailed morphological studies, it was demonstrated that this view needs to be reevaluated. In this paper I evaluate the morphology of five Marginopora populations from around the Coral Sea by microCT-scanning. I argue that ecomorphological and ontogenetic variation is smaller than geographic variation in morphology. This forms the basis for the description of three new species, M. santoensis nov. spec., M. charlottensis nov. spec., M. orpheusensis nov. spec. Quantitative morphological variation between M. rossi, M. orpheusensis nov. spec. and M. charlottensis nov. spec. is overlapping, but each species has unique morphological characters supporting recognition as new species. Support to distinguish the deep living (M. rossi, M. charlottensis nov. spec., M. orpheusensis nov. spec.) and shallow living (M. vertebralis) Marginopora populations as separate species is strong, but not enough molecular phylogenetic data are available to test the three new deep-living species on the Great Barrier Reef hypothesis. However, detailed understanding of ecophenotypic variation in M. santoensis nov. spec. supports the conclusion that it is unlikely that ecophenotypic variation can explain the morphological variation between the three species. I argue that the number of species in this genus is underestimated, and that there are at least five species in the Coral Sea area alone. [ABSTRACT FROM AUTHOR]

The Amazon basin harbors a megadiverse fish fauna spread in an intricate network of big rivers and small streams. The Amazonian streams are home of many small sized fishes that remains poorly documented. In order to accelerate the scientific knowledge on these important aquatic systems we adopted a modern integrative approach joining morphology and molecular tools to investigate the ichthyofauna assemblages from low order streams situated on the lower Tapajós River Basin. Cytochrome c Oxidase I (COI) DNA barcodes from 252 specimens collected from 10 stream sites were obtained. The combined analysis revealed 29 species, 21 genera and 11 families. Cryptic diversity was evidenced in Knodus sp.1, Aequidens epae and Copella callolepis, in which deep genetic divergence were detected (intraspecific distances: 20.48%, 7.99% and 3.77%, respectively). The putative new species showed closer relationships with their counterparts occurring in the Tapajós-Xingu water drainages. [ABSTRACT FROM AUTHOR]

The olive moth -Prays oleae Bern.- remains a significant pest of olive trees showing situation dependent changes in population densities and in severity of damages. The genetic variability of olive moth was assessed on three main olive orchards regions in Portugal by three different markers (COI, nad5 and RpS5), suggesting high species diversity albeit with no obvious relation with a regional pattern nor to an identified ecological niche. Selected COI sequences obtained in this study were combined with those available in the databases for Prays genus to generate a global dataset. The reconstruction of the Prays phylogeny based on this marker revealed the need to revise Prays oleae to confirm its status of single species: COI data suggests the co-existence of two sympatric evolutionary lineages of morphologically cryptic olive moth. We show, however, that the distinct mitochondrial subdivision observed in the partial COI gene fragment is not corroborated by the other DNA sequences. There is the need of understanding this paradigm and the extent of Prays variability, as the disclosure of lineage-specific differences in biological traits between the identified lineages is fundamental for the development of appropriate pest management practices. [ABSTRACT FROM AUTHOR]

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some authors have synonymized all members of the B. fervidus SC within a single taxon, while others propose an alternative two taxa hypothesis. Operating under the phylogenetic species concept, our analysis supports the hypothesis that there are two independent lineages of bumble bees within the B. fervidus SC. With the current evidence, however, it is not possible to assign valid names to either of them, because both lineages include the color phenotypes found in the original species descriptions of B. fervidus and B. californicus. Cryptic speciation does not seem to be the product of Müllerian mimicry between the clades, because diverging coloration patterns are observed when the distribution of the clades overlaps. Furthermore, within each lineage there is evidence for strong population differentiation that is correlated with geographic distribution rather than color phenotype. In our study, we demonstrate the importance of obtaining a broad sample of multiple populations when conducting lower-level phylogenetic analyses. In addition to improving our knowledge of bumble bee diversification patterns, characterizing the evolutionary history of these pollinators provides the foundation needed to guide contemporary conservation assessments and management strategies. [ABSTRACT FROM AUTHOR]

Cryptic species are a challenge for systematics, but their elucidation also may leave critical information gaps about the distribution, conservation status, and behavior of affected species. We use the leopard frogs of the eastern U.S. as a case study of this issue. We refined the known range of the recently described Rana kauffeldi, the Atlantic Coast Leopard Frog, relative to the region’s two other leopard frog species, conducted assessments of conservation status, and improved methods for separating the three species using morphological field characters. We conducted over 2,000 call and visual surveys and took photographs of and tissue samples from hundreds of frogs. Genetic analysis supported a three-species taxonomy and provided determinations for 220 individual photographed frogs. Rana kauffeldi was confirmed in eight U.S. states, from North Carolina to southern Connecticut, hewing closely to the Atlantic Coastal Plain. It can be reliably differentiated in life from R. pipiens, and from R. sphenocephala 90% of the time, based on such characters as the femoral reticulum patterning, dorsal spot size and number, and presence of a snout spot. However, the only diagnostic character separating R. kauffeldi from R. sphenocephala remains the breeding call described in 2014. Based on our field study, museum specimens, and prior survey data, we suggest that R. kauffeldi has declined substantially in the northern part of its range, but is more secure in the core of its range. We also report, for the first time, apparent extirpations of R. pipiens from the southeastern portion of its range, previously overlooked because of confusion with R. kauffeldi. We conclude with a generalized ecological research agenda for cryptic species. For R. kauffeldi, needs include descriptions of earlier life stages, studies of niche partitioning with sympatric congeners and the potential for hybridization, and identification of conservation actions to prevent further declines. [ABSTRACT FROM AUTHOR]

Spanning nearly 13,000 km, the Palearctic region provides an opportunity to examine the level of geographic coverage required for a DNA barcode reference library to be effective in identifying species with broad ranges. This study examines barcode divergences between populations of 102 species of Lepidoptera from Europe and South Siberia, sites roughly 6,000 km apart. While three-quarters of these species showed divergence between their Asian and European populations, these divergence values ranged between 0–1%, distinctly less than the distance to the Nearest-Neighbor species in all but a few cases. Our results suggest that further taxonomic studies may be required for 16 species that showed either extremely low interspecific or high intraspecific variation. For example, seven species pairs showed low or no barcode divergence, but four of these cases are likely to reflect taxonomic over-splitting while the others involve species pairs that are either young or show evidence for introgression. Conversely, some of the nine species with deep intraspecific divergence at varied spatial levels may include overlooked species. Although these 16 cases require further investigation, our overall results indicate that barcode reference libraries based on records from one locality can be very effective in identifying specimens across an extensive geographic area. [ABSTRACT FROM AUTHOR]

Microorganisms, including rotifers, are thought to be capable of long distance dispersal. Therefore, they should show little population genetic structure due to high gene flow. Nevertheless, substantial genetic structure has been reported among populations of many taxa. In rotifers, genetic studies have focused on planktonic taxa leaving sessile groups largely unexplored. Here, we used COI gene and ITS region sequences to study genetic structure and delimit cryptic species in two sessile species (Limnias melicerta [32 populations]; L. ceratophylli [21 populations]). Among populations, ITS region sequences were less variable as compared to those of the COI gene (ITS; L. melicerta: 0–3.1% and L. ceratophylli: 0–4.4%; COI; L. melicerta: 0–22.7% and L. ceratophylli: 0–21.7%). Moreover, L. melicerta and L. ceratophylli were not resolved in phylogenetic analyses based on ITS sequences. Thus, we used COI sequences for species delimitation. Bayesian Species Delimitation detected nine putative cryptic species within L. melicerta and four putative cryptic species for L. ceratophylli. The genetic distance in the COI gene was 0–15.4% within cryptic species of L. melicerta and 0.5–0.6% within cryptic species of L. ceratophylli. Among cryptic species, COI genetic distance ranged 8.1–21.9% for L. melicerta and 15.1–21.2% for L. ceratophylli. The correlation between geographic and genetic distance was weak or lacking; thus geographic isolation cannot be considered a strong driver of genetic variation. In addition, geometric morphometric analyses of trophi did not show significant variation among cryptic species. In this study we used a conservative approach for species delimitation, yet we were able to show that species diversity in these sessile rotifers is underestimated. [ABSTRACT FROM AUTHOR]

The slipper limpet Crepipatella dilatata, native to Chile and Argentina, was introduced in Spain in 2005. The species was thought to inhabit the region of Rias Bajas, yet recently, putative C. dilatata populations have been documented on the coast of north-central Spain and in the Ebro Delta of the Spanish Mediterranean. Here we undertook a multidisciplinary approach to study the invasion biology of this species. Specifically, two geographically distant populations, one being a successfully established population from O Grove and the other a declining population from Gijon, were studied over the course of four years. Analyses of morphological and developmental traits as well as genetic information confirmed the presence of C. dilatata in these sites. The results revealed polymorphism in anatomical traits and shell shape. Shell shape polymorphism was unevenly distributed among sites and among sexes. Males were monomorphic, while females were polymorphic. Of the female morphotypes encountered, one was absent in the declining population from Gijón. Size at first female maturation and female size were greater in the declining population than in the established population. Reproductive success varied seasonally but not spatially among populations. In the established population, gregariousness was significantly greater; the size when sex changes was found to be plastic and socially controlled. The sex ratio of the declining population was female biased while in the established population the sex ratio changed during the study period from being balanced to being female biased. This change in sex ratio was probably due to higher male mortality. Molecular analyses pointed to the localities of Corral Bay in southern Chile and Puerto Madryn in southern Argentina as potential population sources. The intercontinental import of fresh mussels cultivated in Chilean farms is a likely source of this mussel in Spain. Comparison with available data of native populations of C. dilatata strongly indicate that ecophenotypic plasticity, socially controlled sex change, high gregariousness, increased nurse egg supply to viable larvae during the encapsulated developmental period, later maturation and larger female sizes altogether enhance establishment success of this non-indigenous species. Human-mediated factors like the intraregional mussel trade and transplantation are also likely secondary dispersal mechanisms favouring the spread of this organism. [ABSTRACT FROM AUTHOR]

Cassava is a staple food for people across sub-Saharan Africa. Over the last 20 years, there has been an increased frequency of outbreaks and crop damage in this region caused by the cassava-adapted Bemisia tabaci putative species. Little is known about when and why B. tabaci adults move and colonize new cassava crops, especially in farming systems that contain a mixture of cultivar types and plant ages. Here, we assessed experimentally whether the age and variety of cassava affected the density of B. tabaci. We also tested whether the age and variety of the source cassava field affected the variety preference of B. tabaci when they colonized new cassava plants. We placed uninfested potted “sentinel” plants of three cassava varieties (Nam 130, Nase 14, and Njule Red) in source fields containing one of two varieties (Nam 130 or Nase 14) and one of three age classes (young, medium, or old). After two weeks, the numbers of nymphs on the sentinel plants were used as a measure of colonization. Molecular identification revealed that the B. tabaci species was sub-Saharan Africa 1 (SSA1). We found a positive correlation between the density of nymphs on sentinel plants and the density of adults in the source field. The density of nymphs on the sentinels was not significantly related to the age of the source field. Bemisia tabaci adults did not preferentially colonize the sentinel plant of the same variety as the source field. There was a significant interactive effect, however, between the source and sentinel variety that may indicate variability in colonization. We conclude that managing cassava source fields to reduce B. tabaci abundance will be more effective than manipulating nearby varieties. We also suggest that planting a “whitefly sink” variety is unlikely to reduce B. tabaci SSA1 populations unless fields are managed to reduce B. tabaci densities using other integrative approaches. [ABSTRACT FROM AUTHOR]

Austrolebias wolterstorffi is a critically endangered annual fish, occurring in temporary ponds in a restricted area of Southern Brazil and Uruguay. Here, we evaluate the levels of genetic diversity and morphometric differentiation presented by A. wolterstorffi, attempting to reconstruct the spatiotemporal scenario by which this species reached their current distribution. Part of the mitochondrial cytochrome b and nuclear rhodopsin genes were characterized and analysed for a set of 122 and 110 specimens, respectively, collected along the entire distribution range of the species. Additionally, shape variations were evaluated for 92 individuals (43 males and 49 females) through geometric morphometric methods. Our analyses demonstrated several cases of significantly high levels of genetic differentiation among individual populations, in an isolation-by-distance pattern of divergence, with at least six different population groups along the Patos-Mirim lagoon. These groups differed by a minimum of 0.9% and a maximum of 2.6% of corrected cyt b nucleotide distances and did not share any mitochondrial haplotype. Such a pattern, added to the slight morphometric differentiation detected for most of the groups, suggests the occurrence of incipient speciation as consequence of allopatric fragmentation. The chronophylogenetic tree performed with the concatenated dataset supported independent oriental and occidental colonization routes, with the population located in the northwest part of the Rio Grande do Sul coastal plain presenting the most ancient divergence. In general, the recovered biogeographic patterns are highly consistent with the records of Quaternary climatic changes and depositional events that have occurred along the area inhabited by the studied species. This allowed us to establish a molecular clock calibration system for Neotropical annual fish. Thus, although the taxonomic status of each of the detected population units needs further study, it is clear that independent conservation strategies must be taken in each of the major areas covered by this study, most of which are located in Brazil. [ABSTRACT FROM AUTHOR]

Successful eradication of invasives is facilitated by early detection and prompt onset of control. However, realizing or verifying that a colonization has occurred is difficult for cryptic species especially at low population densities. Responding to the capture or unconfirmed sighting of a cryptic invasive species, and the associated effort to determine if it indicates an incipient (small, localized) population or merely a lone colonizer, is costly and cannot continue indefinitely. However, insufficient detection effort risks erroneously concluding the species is not present, allowing the population to increase in size and expand its range. Evidence for an incipient population requires detection of ≥1 individual; its absence, on the other hand, must be inferred probabilistically. We use an actual rapid response incident and species-specific detection estimates tied to a known density to calculate the amount of effort (with non-sequential detections) necessary to assert, with a pre-defined confidence, that invasive brown treesnakes are absent from the search area under a wide range of hypothetical population densities. We illustrate that the amount of effort necessary to declare that a species is absent is substantial and increases with decreased individual detection probability, decreased density, and increased level of desired confidence about its absence. Such survey investment would be justified where the cost savings due to early detection are large. Our Poisson-based model application will allow managers to make informed decisions about how long to continue detection efforts, should no additional detections occur, and suggests that effort to do so is significantly higher than previously thought. While our model application informs how long to search to infer absence of an incipient population of brown treesnakes, the approach is sufficiently general to apply to other invasive species if density-dependent detection estimates are known or reliable surrogate estimates are available. [ABSTRACT FROM AUTHOR]

Coexistence of highly similar species is at odds with ecological theory of competition; coexistence, then, requires stabilizing mechanisms such as differences in ecological niche. In the bacterivore nematode Litoditis marina species complex, which occurs associated with macro-algae, four cryptic lineages (Pm I-IV) co-occur in the field along the south-western coast and estuaries of The Netherlands. Here we investigate the temporal and/or spatial niche differentiation in their natural environment using a qPCR-based detection and relative quantification method. We collected different algal species (i.e. two Fucus species and Ulva sp.) and separated algal structures (i.e. receptacula, thalli, non-fertile tips and bladders) at different sampling months and times (i.e. twice per sampling month), to examine differences in microhabitat use between coexisting L. marina species. Results demonstrate that the cryptic species composition varied among different algal species and algal structures, which was also subject to temporal shifts. Pm I dominated on Fucus spp., Pm II showed dominance on Ulva sp., while Pm III overall had the lowest frequencies. Microhabitat partitioning was most pronounced between the two cryptic species which had similar microbiomes (Pm I and Pm II), and less so between the two species which had significantly different microbiomes (Pm I and Pm III), suggesting that species which share the same microhabitats may avoid competition through resource partitioning. The interplay of microhabitat differentiation and temporal dynamics among the cryptic species of L. marina implies that there is a complex interaction between biotic components and abiotic factors which contributes to their coexistence in the field. [ABSTRACT FROM AUTHOR]

Scinax is a speciose genus of Neotropical hylid frogs. We describe a new species from western Ecuador (elevations between 0 and 1207 m) using morphology, vocalizations, and DNA sequences. We also present a new phylogeny for Scinax based on mitochondrial DNA genes 12S rRNA, Cytochrome Oxidase sub-unit I, Cytochrome B, 16S rRNA, NADH dehydrogenase subunit 1, and adjacent tRNAs. The new species, Scinax tsachila sp. nov. was previously confused with S. quinquefasciatus, a morphologically similar sympatric species. They differ by having markedly different advisement calls, distinct skin texture in the dorsum, and different bone coloration. The new species is sister to S. elaeochroa, a species that differs in advertisement call and color pattern. We provide an updated species account for Scinax quinquefasciatus and a redescription of its holotype. [ABSTRACT FROM AUTHOR]

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key. [ABSTRACT FROM AUTHOR]

The phylogeographic structure of insect species in North America is poorly understood. The moth family Sesiidae (Lepidoptera) contains many economically important pests of agriculture and forestry, as well as beneficial species used in biological control. Despite their significance, this study constitutes the first broad-ranging population genetic study on North American sesiids. It probes the population structure of eight species of sesiid moths based on sequence variation in cytochrome c oxidase I (N = 191). Haplotype diversity levels were high in seven of the eight species, while nucleotide diversity varied considerably. Patterns ranged from limited structure and a starburst pattern in the raspberry crown borer Pennisetia marginata to highly geographically structured populations in the peachtree borer Synanthedon exitiosa and the maple callus borer Synanthedon acerni. These varied patterns suggest differing evolutionary histories and dispersal abilities. By elucidating population genetic structure and barriers to dispersal we can begin to devise conservation and management plans. [ABSTRACT FROM AUTHOR]