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AbstractHere we describe a new species of Ochthebius (Cobalius) from marine rockpools of NW Sicily: O. (C.) senczuki sp. n. This species was first discovered on the basis of molecular evidence, but its taxonomic distinction has been subsequently supported by morphological characters. Ochthebius (C.) senczuki sp. n. shows a clear genetic diversity from the known related species, with an average COI p distance ranging from 5.6% to 10.7%; it exhibits only small morphological differences, mostly limited to dorsal punctation, pronotal and elytral outer edge, and (in males) to the mobile part of the median lobe of the aedeagus. The origin of O. (C.) senczuki sp. n. is estimated to lie in the Late Miocene (~9 Mya); the ancestors of this taxon probably remained isolated from populations of the related taxa of the Ochthebius (Cobalius) subinteger and O. (Cobalius) adriaticus complexes during cycles of regressive and transgressive marine phases that occurred in the SW Mediterranean during Late Miocene and Pliocene. The detailed state of the art of members of the O. (Cobalius) adriaticus complex throughout the Central and Eastern Mediterranean rocky coastal areas is also preliminarily discussed.http://zoobank.org/urn:lsid:zoobank.org:pub:CBFA5063-2FBE-488B-8497-E5DA7DCA9361

Here we describe a new species of Ochthebius (Cobalius) from marine rockpools of NW Sicily: O. (C.) senczuki sp. n. This species was first discovered on the basis of molecular evidence, but its taxonomic distinction has been subsequently supported by morphological characters. Ochthebius (C.) senczuki sp. n. shows a clear genetic diversity from the known related species, with an average COI p distance ranging from 5.6% to 10.7%; it exhibits only small morphological differences, mostly limited to dorsal punctation, pronotal and elytral outer edge, and (in males) to the mobile part of the median lobe of the aedeagus. The origin of O. (C.) senczuki sp. n. is estimated to lie in the Late Miocene (~9 Mya); the ancestors of this taxon probably remained isolated from populations of the related taxa of the Ochthebius (Cobalius) subinteger and O. (Cobalius) adriaticus complexes during cycles of regressive and transgressive marine phases that occurred in the SW Mediterranean during Late Miocene and Pliocene. The detailed state of the art of members of the O. (Cobalius) adriaticus complex throughout the Central and Eastern Mediterranean rocky coastal areas is also preliminarily discussed. [ABSTRACT FROM AUTHOR]

Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co‐occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here, we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between‐species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray–Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together, these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia. [ABSTRACT FROM AUTHOR]

Abstract Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co‐occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here, we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between‐species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray–Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together, these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.

The identification of an emerging pathogen in humans can remain difficult by conventional methods such as enrichment culture assays that remain highly selective, require appropriate medium and cannot avoid misidentifications, or serological tests that use surrogate antigens and are often hampered by the level of detectable antibodies. Although not originally designed for this purpose, the implementation of polymerase-chain-reaction (PCR) has resulted in an increasing number of diagnostic tests for many diseases. However, the design of specific molecular assays relies on the availability and reliability of published genetic sequences for the target pathogens as well as enough knowledge on the genetic diversity of species and/or variants giving rise to the same disease symptoms. Usually designed for clinical isolates, molecular tests are often not suitable for environmental samples in which the target DNA is mixed with a mixture of environmental DNA. A key challenge of such molecular assays is thus to ensure high specificity of the target genetic markers when focusing on clinical and environmental samples in order to follow the dynamics of disease transmission and emergence in humans. Here we focus on the Buruli ulcer (BU), a human necrotizing skin disease mainly affecting tropical and subtropical areas, commonly admitted to be caused by Mycobacterium ulcerans worldwide although other mycolactone-producing mycobacteria and even mycobacterium species were found associated with BU or BU-like cases. By revisiting the literature, we show that many studies have used non-specific molecular markers (IS2404, IS2606, KR-B) to identify M. ulcerans from clinical and environmental samples and propose that all mycolactone-producing mycobacteria should be definitively considered as variants from the same group rather than different species. Importantly, we provide evidence that the diversity of mycolactone-producing mycobacteria variants as well as mycobacterium species potentially involved in BU or BU-like skin ulcerations might have been underestimated. We also suggest that the specific variants/species involved in each BU or BU-like case should be carefully identified during the diagnosis phase, either via the key to genetic identification proposed here or by broader metabarcoding approaches, in order to guide the medical community in the choice for the most appropriate antibiotic therapy. [ABSTRACT FROM AUTHOR]

Island biogeography can promote rapid diversification and speciation via geographic isolation and novel selection pressures. These same factors can threaten the persistence of island endemics by limiting gene flow and suitable habitat. Host-parasite interactions on islands introduce another dimension of complexity as both species must simultaneously adapt to exogenous and endogenous factors. One example of host-parasite island biogeography is the critically endangered Vancouver Island (VI) marmot (Marmota vancouverensis) which is endemic to VI, Canada, and hosts two enteric helminth parasites: Baylisascaris laevis, an ascarid nematode common in tribe Marmotini, and Diandrya vancouverensis, an anoplocephalid cestode endemic to the VI marmot. Here, we aligned novel sequences from B. laevis (six genes) and D. vancouverensis (two genes) with congeneric sequences from GenBank. Phylogenies reconstructed using Bayesian and maximum parsimony approaches consistently placed B. laevis in a morphoclade, and D. vancouverensis in a monophyletic clade sister to D. composita. Mean pairwise sequence divergence between D. vancouverensis and D. composita (9.06 ± 1.94%) surpassed commonly accepted thresholds for species delimitation, whereas divergence between VI and mainland populations of B. laevis (1.12 ± 0.78%) was comparable to (or sometimes greater than) pairwise divergence values between other Baylisascaris species. Disparity in the genetic divergence of each parasite may reflect differences in their life cycle, host specificity, virulence, and the chronological extent of their isolation. Detailed descriptions of the population genetic structure and effects of both parasites on their shared host are crucial next steps in understanding the history of B. laevis and D. vancouverensis on VI and informing conservation efforts for the VI marmot and its enteric helminth parasites.

Moon jellies are some of the most popular, widely distributed, and best-studied marine jellyfish. By the end of the past century only two or three Aurelia species were recognized, but with the rise of DNA barcoding studies, around thirty Aurelia species are presently accepted. Most of the species are morphologically indistinguishable and have restricted biogeography. We reveal, with COI, 16S, and ITS1-5.8S sequence data, two (pseudo-)cryptic species of Aurelia, potentially endemic to the Azores ecoregion, herein provisionally classified as A. "cf. pseudosolida" and A. "misteriosa". These species are closely related to the Mediterranean lineages of A. pseudosolida and A. persea, respectively. In the Azores, the shape of the campanula and oral arms readily distinguishes the two species: the former with folded oral arms and globose campanula, and the latter with flattened campanula and thick and long oral arms. Previous reports of A. solida and A. aurita in the Azores should generally correspond to A. "misteriosa" and A. cf. pseudosolida, respectively. The phylogenetic (re-)examination of the available DNA barcodes of Aurelia only evidenced human-mediated dispersal for A. coerulea, A. relicta, and A. aurita. Aurelia solida cannot be yet considered NIS in the Mediterranean. More jellyfish DNA (meta)barcoding should reveal further cryptic diversity, biological invasions, and phylogeographic inferences. [ABSTRACT FROM AUTHOR]

The Green River in Kentucky in the eastern United States is a freshwater mussel biodiversity hotspot, with 71 known species. Among them, the endangered Pleurobema plenum coexists with other morphologically similar species in the genera Fusconaia and Pleurobema, known colloquially as "pigtoes." Identification of species in these genera is challenging even for mussel experts familiar with them. In our study, the correct identification of these species by experts ranged from 57% to 83%. We delineated taxonomic boundaries among seven species and tested for cryptic biodiversity among these look‐alike mussels utilizing mitochondrial and nuclear DNA sequence variation. Phylogenetic analysis of combined (1215 bp) mitochondrial DNA cytochrome oxidase I (COI) and NADH dehydrogenase 1 (ND1) genes showed five well‐diverged groups that included F. flava, F. subrotunda, P. cordatum, and P. plenum as distinct clades, with P. sintoxia and P. rubrum grouped into a single clade. While our mitochondrial DNA analyses did not distinguish P. sintoxia and P. rubrum as phylogenetically distinct species, the typical shell forms of these two nominal taxa are very distinct. Further phylogenetic analysis using nuclear ribosomal transcribed spacer region subunit I (ITS1) DNA sequences also showed that P. sintoxia and P. rubrum were not distinct lineages. No cryptic species were detected in the Fusconaia and Pleurobema samples analyzed from the Green River. The highest haplotype diversity (h), average number of nucleotide differences (k), and nucleotide diversity (π) were observed for F. subrotunda at both the COI (h = 0.896, k = 3.805, π = 0.00808) and ND1 (h = 0.984, k = 6.595, π = 0.00886) markers, with similarly high genetic diversity in the other taxa. Our results give managers confidence that cryptic taxa do not occur within or among these morphologically similar species in the Green River, and populations appear genetically diverse, indicative of large and healthy populations. [ABSTRACT FROM AUTHOR]

Island biogeography can promote rapid diversification and speciation via geographic isolation and novel selection pressures. These same factors can threaten the persistence of island endemics by limiting gene flow and suitable habitat. Host-parasite interactions on islands introduce another dimension of complexity as both species must simultaneously adapt to exogenous and endogenous factors. One example of host-parasite island biogeography is the critically endangered Vancouver Island (VI) marmot (Marmota vancouverensis) which is endemic to VI, Canada, and hosts two enteric helminth parasites: Baylisascaris laevis , an ascarid nematode common in tribe Marmotini, and Diandrya vancouverensis , an anoplocephalid cestode endemic to the VI marmot. Here, we aligned novel sequences from B. laevis (six genes) and D. vancouverensis (two genes) with congeneric sequences from GenBank. Phylogenies reconstructed using Bayesian and maximum parsimony approaches consistently placed B. laevis in a morphoclade, and D. vancouverensis in a monophyletic clade sister to D. composita. Mean pairwise sequence divergence between D. vancouverensis and D. composita (9.06 ± 1.94%) surpassed commonly accepted thresholds for species delimitation, whereas divergence between VI and mainland populations of B. laevis (1.12 ± 0.78%) was comparable to (or sometimes greater than) pairwise divergence values between other Baylisascaris species. Disparity in the genetic divergence of each parasite may reflect differences in their life cycle, host specificity, virulence, and the chronological extent of their isolation. Detailed descriptions of the population genetic structure and effects of both parasites on their shared host are crucial next steps in understanding the history of B. laevis and D. vancouverensis on VI and informing conservation efforts for the VI marmot and its enteric helminth parasites. [Display omitted] • First nDNA and mtDNA sequences for Baylisascaris laevis and Diandrya vancouverensis. • B. laevis was sister to B. procyonis (raccoon). • B. laevis from Vancouver Island was divergent from the mainland. • Diandrya vancouverensis was a unique species, endemic to Marmota vancouverensis. • Parasites of endangered hosts are also at risk and represent cryptic biodiversity. [ABSTRACT FROM AUTHOR]

Abstract The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.

Species delimitation by traditional morphological methods is challenging in cephalopods due to their flexible bodies, changeable pigment traits, and sometimes high morphological homoplasy. Molecular information provides important assistance for taxonomic decision. In this study, we applied three species delimitation methods on 132 cephalopods from 7 families along Chinese waters, and we found anunderestimated species diversity in these taxa. A maximum of 56 molecular operational taxonomic units was detected, and possible cryptic diversities were revealed in Loliolus beka, Uroteuthis edulis, Octopus minor, Amphioctopus fangsiao, and Hapalochlaena lunulate. This study provides molecular evidence for the hidden species diversity along Chinese waters, and it provides insight into further taxonomic research on these morphologically variable taxa.

The genus Pseudoblepharisma is currently comprised of only one species, P. tenue, and one variant, P. tenue var. viride, both described as free-living ciliates thriving in oxygen depleted freshwater habitats of Europe. Here we report on this genus being discovered from subtropical freshwaters of Florida, USA. The Florida strain diverges from the P. tenue by being much larger, as well as having a far higher density of intracellular symbiotic green algae, resembling P. tenue var. viride. Unlike its European counterparts, the North American strain was observed to build a lorica, likely useful for protection and feeding; this has not been previously described for this genus. In contrast to P. tenue, the Florida strain does not have endosymbiotic purple bacteria. Despite large distances between sampling zones, the species is a close match at a morphological level to Pseudoblepharisma tenue var. viride. We provide the first 18S rRNA gene sequence for this species, allowing future investigations into the biogeography of this genus. As intensive sampling efforts continue to increase, cryptic microbial species will continue to be recorded from diverse freshwater habitats at a global scale. [ABSTRACT FROM AUTHOR]

Moon jellies are some of the most popular, widely distributed, and best-studied marine jellyfish. By the end of the past century only two or three Aurelia species were recognized, but with the rise of DNA barcoding studies, around thirty Aurelia species are presently accepted. Most of the species are morphologically indistinguishable and have restricted biogeography. We reveal, with COI, 16S, and ITS1-5.8S sequence data, two (pseudo-)cryptic species of Aurelia, potentially endemic to the Azores ecoregion, herein provisionally classified as A. “cf. pseudosolida” and A. “misteriosa”. These species are closely related to the Mediterranean lineages of A. pseudosolida and A. persea, respectively. In the Azores, the shape of the campanula and oral arms readily distinguishes the two species: the former with folded oral arms and globose campanula, and the latter with flattened campanula and thick and long oral arms. Previous reports of A. solida and A. aurita in the Azores should generally correspond to A. “misteriosa” and A. cf. pseudosolida, respectively. The phylogenetic (re-)examination of the available DNA barcodes of Aurelia only evidenced human-mediated dispersal for A. coerulea, A. relicta, and A. aurita. Aurelia solida cannot be yet considered NIS in the Mediterranean. More jellyfish DNA (meta)barcoding should reveal further cryptic diversity, biological invasions, and phylogeographic inferences.

The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding. [ABSTRACT FROM AUTHOR]

Tropical islands hold great treasures of Earth's biodiversity, but these fragile ecosystems may be lost before their diversity is fully catalogued or the evolutionary processes that birthed it are understood. We ran comparative analyses on the ND2 and ND3 mitochondrial genes of the Sulawesi babbler Pellorneum celebense , an understorey bird endemic to Sulawesi and its continental islands, along with its morphology and song. Genetic, acoustic, and morphological data agree on multiple isolated populations, likely representing independently evolving lineages. The Sulawesi babbler shows signs of rapid speciation, with populations diverging between Central and Southeast Sulawesi, and even on land-bridge islands which were connected within the last few tens of thousands of years. The genetic divergence between Sulawesi babbler populations in this time has been around 33% of their divergence from sister species which have been isolated from Sulawesi for millions of years. This is likely facilitated by the Sulawesi babbler's understorey lifestyle, which inhibits gene flow and promotes speciation. Similar patterns of endemism are seen in Sulawesi's mammals and amphibians. This work highlights the undocumented biodiversity of a threatened hotspot, wrought by complex processes of speciation which interact with ecology and geology. Subspecific taxonomy has at times been controversial, but we argue that discrete populations such as these play a key role in evolution. Lying as they do at the heart of the biodiversity hotspot of Wallacea, these islands can reveal much about the evolution of biodiversity at all of its levels, from the gene to the ecosystem. [ABSTRACT FROM AUTHOR]

A molecular and morphological taxonomic study of Corallina (Corallinales, Rhodophyta) from Tristan da Cunha and the Falkland Islands revealed Corallina chamberlainiae J.Brodie & R.Mrowicki sp. nov. from both South Atlantic archipelagos, and Corallina cf. caespitosa only in the Falkland Islands. Analysis of mitochondrial COI-5P and plastid psbA resolved C. chamberlainiae as a distinct clade composed of specimens from Tristan and the Falkland Islands (COI-5P), in addition to two matching New Zealand samples (psbA). In psbA analyses, C. cf. caespitosa was close to two species from Japan (as C. pilulifera and C. melobesioides) but was separate from C. caespitosa sensu stricto from Britain and C. ferreyrae (isotype) from Peru. In COI-5P analyses, C. cf. caespitosa was in a clade with C. caespitosa (holotype) and close to, but distinct from, C. ferreyrae and an unidentified South African Corallina species. Application of the Automatic Barcode Gap Discovery (ABGD) and Poisson tree processes (bPTP) for COI-5P lumped C. chamberlainiae into one clade, whereas the Generalized Mixed Yule Coalescent (GMYC) model split it into two well-supported groups, one of which only contained Falkland Island specimens. All three models lumped C. cf. caespitosa with C. caespitosa. C. chamberlainiae closely resembles C. officinalis, the generitype, but is distinguished by smaller size and a more compressed thallus towards the apex. Corallina cf. caespitosa resembles C. caespitosa but is smaller and has fused, palm-like upper fronds. Neither of these taxa is conspecific with C. ferreyrae although C. caespitosa was recently synonymized with C. ferreyrae. C. chamberlainiae and C. cf. caespitosa occupy similar intertidal habitats to their respective, closely related counterparts C. officinalis and C. caespitosa. The results indicate cryptic diversity and suggest that there are many misidentified Corallina species. The paucity of South Atlantic studies of the Corallinales points to the need for a much greater taxonomic effort in this biogeographic region. [ABSTRACT FROM AUTHOR]

Premise: Whole‐genome duplication (polyploidy) is an important force shaping flowering‐plant evolution. Ploidy‐specific plant–pollinator interactions represent important community‐level biotic interactions that can lead to nonrandom mating and the persistence of mixed‐ploidy populations. Methods: At a naturally occurring diploid–tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee‐collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy‐specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa have ploidy‐specific visitation and pollen collection biases. Results: Although bee assemblages overlapped, we found significant differences in bee visitation to co‐occurring diploids and tetraploids, with the introduced honeybee (Apis mellifera) and one native species (Andrena species 12) more frequently visiting tetraploids. Consistent with bee assemblage differences, we found that diploid pollen was overrepresented among pollen loads on native bees, while pollen loads on A. mellifera did not deviate from the random expectation. However, mismatches between the ploidy of pollen loads and plants were common, consistent with ongoing intercytotype gene flow. Conclusions: Our data are consistent with cytotype‐specific bee visitation and suggest that pollinator behavior contributes to reduced diploid–tetraploid mating. Differences in bee visitation and pollen movement potentially contribute to an easing of minority cytotype exclusion and the facilitation of cytotype co‐occurrence. [ABSTRACT FROM AUTHOR]

The genus Pseudoblepharisma is currently comprised of only one species, P. tenue, and one variant, P. tenue var. viride, both described as free-living ciliates thriving in oxygen depleted freshwater habitats of Europe. Here we report on this genus being discovered from subtropical freshwaters of Florida, USA. The Florida strain diverges from the P. tenue by being much larger, as well as having a far higher density of intracellular symbiotic green algae, resembling P. tenue var. viride. Unlike its European counterparts, the North American strain was observed to build a lorica, likely useful for protection and feeding; this has not been previously described for this genus. In contrast to P. tenue, the Florida strain does not have endosymbiotic purple bacteria. Despite large distances between sampling zones, the species is a close match at a morphological level to Pseudoblepharisma tenue var. viride. We provide the first 18S rRNA gene sequence for this species, allowing future investigations into the biogeography of this genus. As intensive sampling efforts continue to increase, cryptic microbial species will continue to be recorded from diverse freshwater habitats at a global scale.

We report ecological observations of Bolitoglossa altamazonica and B. peruviana in the Peruvian Amazon with suggestions on their conservation. Two localities are provided for both species in one protected area, Allpahuyo-Mishana National Reserve and in Puerto Almendra near the city of Iquitos, northern Peru. A different type of B. altamazonica was also discovered in Allpahuyo-Mishana. It is similar to B. madeira with a reddish coloration on the dorsal parts. Another «grey» type was also reported living between Puno and Madre de Dios departments at higher elevations. However, all the specimens found through their range in Peru have shown colour variation which complicates species identification. New taxonomic studies are needed to confirm their status. The Peruvian salamanders appear to be semi-arboreal species living in primary unflooded terra firme rainforests near water bodies where humidity is high at lower elevations as previously reported (96–118 m a.s.l.). Despite most of the Bolitoglossa species occur in protected areas, a deadly threat was recently reported in frogs (Batrachochytridium dendrobatidis) that may cause loss of salamanders in Peru. For example during our field surveys we were unable to observe B. digitigrada. New assessments are urgently needed for the protection and conservation of Peruvian salamanders. Data on biology, ecology and environmental parameters are also lacking to really protect their microhabitats, and to establish suitable ex situ keeping and breeding programs with the difficult perspective of subsequent reintroduction.

• Target enrichment can directly sequence host-associated fungal pathogens. • Fungal pathogen load is positively associated with enrichment success. • Resulting genetic data can identify phylogenetic placements of fastidious strains. • Salamander at US zoo was infected with Asian-origin Batrachochytrium strain. • Method can be applied to other unculturable fungal samples to identify cryptic strains. The chytrid fungus Batrachochytrium dendrobatidis (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (Rana) from North America, and (2) a Japanese Giant Salamander (Andrias japonicus) at the Smithsonian Institution's National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the Rana -derived strains in the Bd-GPL clade. In contrast, the A. japonicus strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild A. japonicus and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches. [ABSTRACT FROM AUTHOR]

Octospora conidiophora is described as a new species, based on collections from South Africa. It is characterised by apothecia with a distinct margin, smooth or finely warted ellipsoid ascospores, stiff, thick-walled hyaline hairs, warted mycelial hyphae and growth on pleurocarpous mosses Trichosteleum perchlorosum and Sematophyllum brachycarpum (Hypnales) on decaying wood in afromontane forests. It is the first species of bryophilous Pezizales in which an anamorph has been observed; it produces long, claviform, curved, hyaline and transversely septate conidia. Three other cryptic species of Octospora were detected using three molecular markers (LSU and SSU nrDNA and EF1α), but these could not be distinguished phenotypically. These are not described formally here and an informal species aggregate O. conidiophora agg. is established for them. The new species and finds of Lamprospora campylopodis growing on Campylopus pyriformis and Neottiella albocincta on Atrichum androgynum represent the first records of bryophilous Pezizales in South Africa. [ABSTRACT FROM AUTHOR]

The full extent of sympatric intraspecific population diversity (SIPD) i.e. structuring into multiple genetically distinct Mendelian populations, remains uncertain for most lacustrine fish species, particularly in northern lakes. However, increasing application of molecular genetics is advancing understanding and has shown both that many known intraspecific sympatric lacustrine morphological and behavioural polymorphisms represent SIPD, and resolved the existence of phenotypically cryptic structuring.Uncertainty remains as only a few northern lakes have been comprehensively surveyed and existing studies focus on known phenotypic polymorphisms or exploit ad hoc field sampling, marker selection and data analysis methods. Such unfocused approaches constrain resolving power and increase the likelihood of failing to detect SIPD when present.Brown trout (Salmo trutta L.) in a previously unstudied Scottish lake were collected by 3D stratified random netting. They were screened with both an arbitrary set of molecular markers and markers pre‐selected for their ability to resolve regional allopatric brown trout population structuring and data analysed by both Bayesian and non‐Bayesian approaches.Depth clines for mitochondrial and microsatellite markers variation were observed and found to arise from different, but overlapping, depth distributions of four genetically distinct piscivorous, limnetic, shallow benthic, and profundal benthic populations. This is the highest number of ecologically and phenotypically distinct sympatric brown populations identified in any lake to date, and includes the first reported profundal benthic form.The detection of the SIPD in Loch Laidon depended critically on the random 3D sampling and using markers preselected for their power to differentiate regional allopatric populations of trout, as well as aided by using both Bayesian and non‐Bayesian analytical approaches.The findings support the view that the extent of ecologically and evolutionarily significant SIPD is probably underestimated in brown trout and other fish species, and probably is a significant component of the biodiversity in many northern hemisphere lakes. [ABSTRACT FROM AUTHOR]

We developed novel microsatellite markers for D alechampia scandens L. ( Euphorbiaceae). The target plants belong to a distinct, but undescribed, species in the D . scandens species complex, characterized by small resin-producing glands. In total, 110 alleles over 36 novel markers were identified across 39 individuals from three populations. The number of alleles varied from one to seven, with an average of 3.06 ± 0.26 alleles per locus. The developed markers, along with previously developed ones for a large-glanded D . scandens species, were tested for amplification in 11 additional species of the genus D alechampia. Four markers did not produce any detectable allele in 37 individuals from two populations of the large-glanded species. Average expected heterozygosity across all small- and large-glanded specific loci was 0.36 and 0.15, for the small and large glanded populations, respectively. Cross-species amplification showed that 89% of all markers were successfully amplified in at least one of the 11 other D alechampia species. These microsatellite markers may be useful for detecting undescribed species in the D . scandens species complex, and can be used for comparative analyses of genetic structure, mating system and phylogeography of other D alechampia species. [ABSTRACT FROM AUTHOR]

Southern Africa is a marine biodiversity hotspot that not only comprises faunal elements from the Atlantic and Indian Oceans, but also large numbers of endemic species. Using mitochondrial and nuclear DNA sequence data, we explored whether genetic structure in the endemic coastal goby Psammogobius knysnaensis, a species whose range straddles both biomes, is linked to the boundary between the two oceans. Subtle genetic structure was identified between Atlantic and Indian Ocean populations, with genetic diversity being lower in the Atlantic, and particularly on the west coast. Our results point to partial isolation between the populations associated with each biome that is most likely driven by the region's oceanography, but unlike in other species, there is no evidence for distinct regional evolutionary lineages that are likely adapted to the environmental conditions prevalent in each region. The exclusive presence of P. knysnaensis in sheltered habitats (estuaries and lagoons) may protect this species from the severe impacts of cold water upwelling on the west coast. [ABSTRACT FROM AUTHOR]

DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long-wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character-based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character-based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character-based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character-based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character-based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost-efficient approach to estimate presence, absence or frequency of cryptic species. [ABSTRACT FROM AUTHOR]

[Display omitted] • Phylogenetic analysis reveals a high lineage diversity of Sphaeridae in Japan. • Analyses suggest Japanese Sphaeriidae consist of at least 18 delimitated lineages. • Many lineages have been observed only in Japan. • Sphaeriid diversity may result from both ancient colonisations and recent dispersals. Revealing the species and lineage diversity of a taxon is important for many biological studies of wildlife. In recent decades, DNA-based approaches have been widely utilised to elucidate the diversity of taxa, especially those that are difficult to distinguish based on morphological traits. This study focused on freshwater clams (Sphaeriidae) in Japan, a biodiversity hotspot of freshwater molluscs. Molecular phylogenetic approaches, including divergence time estimation, species delimitation, rarefaction, and biogeographic area estimation, were used to reveal the nature of the species diversity and its formation process, which are largely unknown. Our delimitation and rarefaction analyses suggest that Japanese sphaeriid clams consist of at least 18 delimitated lineages. This lineage diversity is relatively high compared to other Japanese freshwater molluscs, and in addition, the majority of the Japanese lineage appears to have high endemicity despite the possibility of long-distance dispersal in sphaeriid clams. Our biogeographical analyses suggest that this diversity may be due to the combination of colonisation, during the period when Japan was connected to the continent, and the relatively recent dispersal. Our results highlight the overlooked biodiversity of Japan and provide a basis for further Japanese sphaeriid research, including conservation perspectives. [ABSTRACT FROM AUTHOR]

The taxonomy of the genus Ophiocoma was last revised by Devaney in 1970. Recent discoveries of new species and re-instatement of previously synonymized names suggest that we still do not fully understand the species limits in this genus. A recent biodiversity survey of the SW Indian Ocean shallow reefs strongly suggested an unrecognised species in the genus, closely related to O. brevipes/O. dentata. This study examined both the molecular phylogenetic relationships and the morphological characteristics of several species in the genus in order to characterise the unrecognised species. The focal species clusters with O. brevipes, O. dentata, O. doederleini within a monophyletic clade supported by molecular data for the first time. The name Breviturma subgen. nov. is proposed for this clade, previously known as brevipes group. Type material of nominal species that have been synonymized with O. dentata was examined and re-assessed. Ophiocoma marmorata proved not conspecific with O. dentata. A rarely used character, dorsal disc granule density, was tested and showed differences between the examined species at similar sizes. In combination with colour pattern, disc granule density, arm spine sequence and maximum disc size, the new species was delimited morphologically and described as Ophiocoma krohi sp. nov.

An analysis of the variability of 34 sequences of the 5′-region of the Co-1 mitochondrial gene fish of the genus Ammodytes has been performed taking the precise geographic location into account. Among them, seven sequences are original data and 27 were retrieved from the GenBank. Two hypotheses on the taxonomic composition of sand lances of North Pacific have been proposed. The first is preferable to the authors; it assumes that there are four separate species, while the second considers the presence of a complex circumpolar species with four major local geographic races. Both hypotheses suppose a clear delineation and deep divergence of cold-water sand lances from warmer-water southern ones. These data and the analysis of the history of the study of the taxonomy of far-eastern sand lances allowed us to consider that the use of the species name A. personatus is inappropriate for sand lances from the Yellow Sea and the southern part of the Sea of Japan, as well as for some representatives of the Bering sea and the Sea of Okhotsk and adjacent waters, which form a separate monophyletic group with the current name Ammodytes hexapterus. [ABSTRACT FROM AUTHOR]

Abstract: Collyriclum faba (Bremser in Schmalz, 1831) is a monostome digenetic trematode with unknown life cycle. On its definitive bird host, C. faba occurs in pairs within a subcutaneous cyst, the location of which on the host body is the base for differentiating three ecotypes of C. faba. Here we examined the hypothesis connecting strong host-specificity of the ecotypes with the possible existence of cryptic speciation among C. faba. Analysis of conserved nuclear ribosomal DNA regions rejected the cryptic speciation hypothesis. Analyses of the variable ITS1 and ITS2 regions revealed that, despite some differentiation between the ecotypes, several large-scale indels occur in multiple ecotypes. Individuals from multiple cysts affecting each host individual differed in their ITS1 sequences, suggesting the individuals infecting a single host did not have common parents. Since we were the first to sequence C. faba, we attempted to verify its position in the current taxonomic system (Plagiorchiida: Gorgoderoidea). We found that C. faba segregates with the superfamily Microphalloidea (in order of maximum likelihood phylogeny: Prosthogonimidae, Pleurogenidae and Microphallidae) instead of any species of the superfamily Gorgoderoidea, as proposed in the past. The results necessitate reclassification of the family Collyriclidae as a member of Microphalloidea. [Copyright &y& Elsevier]

The Caloplaca holocarpa group contains members of the family Teloschistaceae with a strongly reduced thallus and conspicuous yellow, orange or red apothecia. In the absence of well-defined thallus characters, taxa of this group must be identified mainly by apothecial characters and are as a result often difficult to separate. The species of this group have been shown not to form a monophyletic entity, with representatives of other Teloschistaceae with more complex thalli intermixed among them. Caloplaca skii and C. syvashica are recognized here as two homogeneous clades with Caloplaca holocarpa-like phenotypes. Caloplaca skii, which is widespread in southern Europe, resembles C. cerinelloides but is distinguished by its smaller and narrower ascospores and by growing predominantly on xerophilous shrubs. Caloplaca syvashica is restricted to shrubs in salt marshes in the northern Black Sea region. It is similar to the British Caloplaca suaedae and Australian C. yarraensis, but differs from both, mainly in ascospore characters. Caloplaca yarraensis is closely related to the new C. syvashica but arguments against their conspecificity are emphasised. A key for epiphytic C. holocarpa-like Teloschistaceae from Europe is provided. [ABSTRACT FROM PUBLISHER]

Abstract: Free-living ciliates are a diverse group of microbial eukaryotes that inhabit aquatic environments. They have a vital role within the ‘microbial loop’, being consumers of microscopic prey such as bacteria, micro-algae, and flagellates, and representing a link between the microscopic and macroscopic components of aquatic food webs. This investigation describes the ciliate communities of four habitats located in the catchment of the River Frome, the major chalk-stream in southern Britain. The ciliate communities were characterised in terms of community assemblage, species abundance and size classes. The ciliate communities investigated proved to be highly diverse, yielding a total of 114 active species. An additional 15 ‘cryptic’ ciliate species were also uncovered. Heterogeneity in the ciliate communities was evident at multiple spatial scales, revealing hot spots of species richness, both within and between habitats. The ciliate communities of habitats with flowing water were composed of smaller ciliates compared to the still-water habitats examined. [Copyright &y& Elsevier]