Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade.

Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.

Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak).

Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.

Molecular Data Confirm Interspecific Limits of Four Alloxysta and One Phaenoglyphis Species of Parasitic Wasps within the Subfamily Charipinae (Cynipoidea: Figitidae).

The hymenopteran subfamily Charipinae (Cynipoidea: Figitidae) consist of a group of parasitic wasps that are exclusive hyperparasitoids of Hemipteran. The species boundaries in Charipinae have historically been unclear. While diagnostic morphological features have been established for the stepwise separation of species, it is recommended to confirm those limits using molecular data. Here, we focus on the genera Alloxysta Förster, 1869 and Phaenoglyphis Förster, 1869, both of which contain species that are hyperparasitoids of aphids. We sequenced three genes (mitochondrial COI and 16S rDNA, and nuclear ITS2 rDNA) from specimens that were identified as belonging to five species: Alloxysta brevis (Thomson, 1862), A. castanea (Hartig, 1841), A. ramulifera (Thomson, 1862), A. victrix (Westwood, 1833), and Phaenoglyphis villosa (Hartig, 1841). The phylogeny resulting from concatenating these genes supported the species status of the five morphologically identified taxa, with P. villosa nested within Alloxysta. Our study thus indicates that these molecular markers can successfully distinguish charipine species, and also indicates that the genera Alloxysta and Phaenoglyphis may be more closely related than previously hypothesized. We also present the first estimates of genetic distances for these species. Future studies that include more species, loci, and/or genomic data will complement our research and help determine species relationships within the Charipinae subfamily.

Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae).

Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high-dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.

High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses.

Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism in adult morphology, particularly body coloration and size and shape of the first legs. Consequently, the male and female from the same species might be erroneously assigned to different species or even different genera, which could generate synonymies in classification if only morphological data were used. Phintella is a species-rich genus of Salticidae, which currently exhibits 76 named species. However, the male-female counterpart is unknown for nearly half of the species. In this study, we used a molecular approach to delineate the species boundaries for Phintella and Phintella-like specimens collected in Vietnam, using morphological information as supporting data. We used three gene fragments (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical considerations for species delimitation. A total of 22 putative species were recognized: 18 species of the genus Phintella, one species of the genus Lechia (L. squamata), and three species of the genus Phinteloides. Eleven undescribed species were discovered, of which seven have a male-female combination, two species have only males, and two species have only females. The crown age of Phintella was estimated at the Serravallian stage of the Miocene after the increase of species number around 16 MYA. The crown ages of most putative species recognized in this study were estimated in the Pleistocene, and the divergence among sister species likely occurred from the mid-Miocene to the Pliocene. Our ancestral range reconstruction results showed that the diversification of our ingroup was governed by progressive dispersal events, i.e., Phintella and their related species in Vietnam diversified while expanding their range on the continent. Our results provide fundamental biodiversity data for a high-diversity genus in Vietnamese Phintella spiders.

Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers.

Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35-2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex.

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex.

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

Phylogenetic assessment of endangered and look-alike Pigtoe species in a freshwater mussel diversity hotspot.

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.

Humanising and dehumanising pigs in genomic and transplantation research.

Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to 'humanise' donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that 'humanise' the pig (or representations thereof) through using resources from human genomics, and the need to 'dehumanise' the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this.

A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity.

PREMISE: Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and   thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS: To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS: Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS: The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

Lineage and role in integrative taxonomy of a heterotrophic orchid complex.

Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.

Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species.

BACKGROUND AND AIMS: Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted. METHODS: We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status. KEY RESULTS: All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids. CONCLUSIONS: Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.

Genome architecture used to supplement species delineation in two cryptic marine ciliates.

The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%-0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.

The Ecology of Spider Sociality: A Spatial Model.

AbstractThe emergence of animal societies offers unsolved problems for both evolutionary and ecological studies. Social spiders are especially well suited to address this problem given their multiple independent origins and distinct geographic distribution. On the basis of long-term research on the spider genus Anelosimus, we developed a spatial model that re-creates observed macroecological patterns in the distribution of social and subsocial spiders. We show that parallel gradients of increasing insect size and disturbance (rain, predation) with proximity to the lowland tropical rain forest would explain why social species are concentrated in the lowland wet tropics but absent from higher elevations and latitudes. The model further shows that disturbance, which disproportionately affects small colonies, not only creates conditions that require group living but also tempers the dynamics of large social groups. Similarly simple underlying processes, albeit with different players on a somewhat different stage, may explain the diversity of other social systems.

A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida).

Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (Rhinoptericola Carvajal & Campbell, 1975 and Nataliella Palm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1-D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacantha Carvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray and a species of stingray, and is revealed to have a transatlantic distribution. Data from SEM suggest a simpler interpretation of hook arrangement in the metabasal armature for Rhinoptercola and-in combination with 28S sequence data-support Shirleyrhynchus Beveridge & Campbell, 1988 (a former rhinoptericolid) as its junior synonym. The three species formerly assigned to Shirleyrhynchus are thus transferred to Rhinoptericola. Data from light microscopy on whole-mounted specimens and histological sections, SEM, and 28S showed the eutetrarhynchid Prochristianella jensenae Schaeffner & Beveridge, 2012b to be morphologically consistent with species of Rhinoptericola and it is thus transferred to the genus. The type series of P. jensenae was determined to be mixed, representing two distinct species which are here redescribed and described as new, respectively. Two additional novel species of Rhinoptericola are described from cownose rays from off Mozambique and the Gulf of California.

Phylogenetic relationships among the species of the Cameroonian endemic freshwater crab genus Louisea Cumberlidge, 1994 (Crustacea, Brachyura, Potamonautidae), with notes on intraspecific morphological variation within two threatened species.

Louisea Cumberlidge, 1994 (Crustacea, Brachyura, Potamonautidae) currently includes four endemic Cameroonian freshwater crab species whose phylogenetic relationships were previously unresolved. In the present study, phylogenetic analyses are carried out involving three mtDNA loci (COI, 12S rRNA, and 16S rRNA). The COI locus revealed divergence times of 5.6 million years ago (myr) for when L.balssi (Bott, 1959) diverged from L.edeaensis (Bott, 1969); 4.1 myr for when L.edeaensis diverged from L.yabassi Mvogo Ndongo, von Rintelen & Cumberlidge, 2019; and 2.48 myr for when the later species diverged from L.nkongsamba Mvogo Ndongo, von Rintelen & Cumberlidge, 2019. Three genetic lineages were found within L.nkongsamba that are supported by uncorrected p-distances and the haplotype network. Morphological variation in some taxonomically important characters was found within both L.nkongsamba and L.yabassi. No correlation, however, was found between the morphotypes within these species and the uncovered genetic lineages. Recognition of species boundaries and of subpopulations of species will prove valuable when making informed conservation decisions as part of the development of species action plans for these rare and threatened freshwater crabs.

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance.

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation-related actions.

Type specimen sequencing, multilocus analyses, and species delimitation methods recognize the cosmopolitan Corallina berteroi and establish the northern Japanese C. yendoi sp. nov. (Corallinaceae, Rhodophyta).

A partial rbcL sequence of the lectotype specimen of Corallina berteroi shows that it is the earliest available name for C. ferreyrae. Multilocus species delimitation analyses (ABGD, SPN, GMYC, bPTP, and BPP) using independent or concatenated COI, psbA, and rbcL sequences recognized one, two, or three species in this complex, but only with weak support for each species hypothesis. Conservatively, we recognize a single worldwide species in this complex of what appears to be multiple, evolving populations. Included in this species, besides C. ferreyrae, are C. caespitosa, the morphologically distinct C. melobesioides, and, based on a partial rbcL sequence of the holotype specimen, C. pinnatifolia. Corallina berteroi, not C. officinalis, is the cosmopolitan temperate species found thus far in the NE Atlantic, Mediterranean Sea, warm temperate NW Atlantic and NE Pacific, cold temperate SW Atlantic (Falkland Islands), cold and warm temperate SE Pacific, NW Pacific and southern Australia. Also proposed is C. yendoi sp. nov. from Hokkaido, Japan, which was recognized as distinct by 10 of the 13 species discrimination analyses, including the multilocus BPP.

Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals).

While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the coral community level, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy based largely on skeletal macromorphology has underestimated the diversity of many coral families. Here, we use targeted enrichment methods to sequence 2476 ultraconserved elements (UCEs) and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). Moreover, we analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both F. fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally for H. limax in the Red Sea. By combining UCE/exon data and mitochondrial sequences captured in off-target reads, we reinforce earlier findings that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for taxonomic and systematic re-evaluations of some species and genera within the family Fungiidae. This work demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which we can test phylogenetic hypotheses based on morphological and/or life history traits.

Selection and isolation define a heterogeneous divergence landscape between hybridizing Heliconius butterflies.

Hybridizing species provide a powerful system to identify the processes that shape genomic variation and maintain species boundaries. However, complex histories of isolation, gene flow, and selection often generate heterogeneous genomic landscapes of divergence that complicate reconstruction of the speciation history. Here, we explore patterns of divergence to reconstruct recent speciation in the erato clade of Heliconius butterflies. We focus on the genomic landscape of divergence across three contact zones of the species H. erato and H. himera. We show that these hybridizing species have an intermediate level of divergence in the erato clade, which fits with their incomplete levels of reproductive isolation. Using demographic modeling and the relationship between admixture and divergence with recombination rate variation, we reconstruct histories of gene flow, selection, and demographic change that explain the observed patterns of genomic divergence. We find that periods of isolation and selection within populations, followed by secondary contact with asymmetrical gene flow are key factors in shaping the heterogeneous genomic landscapes. Collectively, these results highlight the effectiveness of demographic modeling and recombination rate estimates to disentangling the distinct contributions of gene flow and selection to patterns of genomic divergence.