RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.

Metazoa-level USCOs as markers in species delimitation and classification

Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.

Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Papilionoideae) in Florida

The importance and prevalence of recent ice-age and post-glacial speciation and species diversification during the Pleistocene across many organismal groups and physiographic settings are well established. However, the extent to which Pleistocene diversification can be attributed to climatic oscillations and their effects on distribution ranges and population structure remains debatable. In this study, we use morphologic, geographic and genetic (RADseq) data to document Pleistocene speciation and intra-specific diversification of the unifoliolate-leaved clade of Florida Lupinus, a small group of species largely restricted to inland and coastal sand ridges across the Florida peninsula and panhandle. Phylogenetic and demographic analyses alongside morphological and geographic evidence suggest that recent speciation and intra-specific divergence within this clade were driven by a combination of non-adaptive allopatric divergence caused by edaphic niche conservatism and opportunities presented by the emergence of new post-glacial sand ridge habitats. These results highlight the central importance of even modest geographic isolation and short periods of allopatric divergence following range expansion in the emergence of new taxa and add to the growing evidence that Pleistocene climatic oscillations may contribute to rapid diversification in a myriad of physiographic settings. Furthermore, our results shed new light on long-standing taxonomic debate surrounding the number of species in the Florida unifoliate Lupinus clade providing support for recognition of five species and a set of intra-specific variants. The important conservation implications for the narrowly restricted, highly endangered species Lupinus aridorum, which we show to be genetically distinct from its sister species Lupinus westianus, are discussed.

An Improved Chromosome-Level Genome Assembly of the Firefly Pyrocoelia pectoralis

The endemic and endangered Chinese firefly Pyrocoelia pectoralis is a sexually dimorphic, nocturnal species. A previous attempt by this team to assemble a draft genome of P. pectoralis using PacBio and Illumina HiSeq X Ten platforms was limited in its usefulness by high redundancy and contamination. This prompted us to conduct an improved chromosome-level genome assembly of P. pectoralis. Ten chromosomes were further assembled based on Hi-C data to a 532.25 Mb final size with a 52.87 Mb scaffold N50. The total repeat lengths in the genome of P. pectoralis amount to 227.69 Mb; 42.78%. In total, 12,789 genes could be functionally annotated using at least one public database. Phylogenetic inference indicated that P. pectoralis and P. pyralis diverged ~51.41 million years ago. Gene family expansion and contraction analysis of 12 species were performed, and 546 expanded and 2660 contracted gene families were identified in P. pectoralis. We generated a high-quality draft of the P. pectoralis genome. This genome assembly should help promote research on the species' sexual dimorphism and its unique courtship behavior, which involves a combination of pheromonal and bioluminescent signals. It also can serve as a resource for accelerating genome-assisted improvements in the conservation of this species.

Bamboozled! Resolving deep evolutionary nodes within the phylogeny of bamboo corals (Octocorallia: Scleralcyonacea: Keratoisididae)

Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups - D1 and D2, and A1 and M1 - needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters.

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

BACKGROUND

Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers.

RESULTS

Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods.

CONCLUSIONS

The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.

Multiple Outgroups Can Cause Random Rooting in Phylogenomics

Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods. The results also indicate that the standard practice of using multiple outgroups often causes random rooting. Most researchers go out of their way to get multiple outgroups, as this has been standard practice for decades. Based on our findings, this practice should stop. Instead, our results suggest that a single (most closely) related relative should be selected as the outgroup, unless all outgroups are roughly equally closely related to the ingroup.

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.

The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey

Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.

Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage

The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.

Revealing the Coral Species Diversity in Xiamen Bay: Spatial Distribution of Genus Astrogorgia (Cnidaria, Alcyonacea, Plexauridae) and Newly Recorded Species

Coral reefs provide a habitat for many marine organisms and support the safety, coastal protection, well-being, and food and economic security of hundreds of millions of people. The focus on coral species diversity cannot be overemphasized. One of them, Astrogorgia, contains many marine natural active substances, and has important scientific research value and application prospects. Most of the current research on the active substances of the genus Astrogorgia is based on unidentified species, and in-depth taxonomic studies are urgently needed. A total of 1185 samples were collected from 2014 to 2021 in the waters of Xiamen Bay. Herein, the morphological identification, electronic microscopy, and gene fragment sequencing methods were used for the taxonomic study. There are three species of Astrogorgia identified, including Astrogorgia lafoa, A. arborea, and A. dumbea. Among them, A. lafoa and A. arborea are newly recorded species in the waters of China. A. lafoa is distributed in Qingyu Island, A. arborea is distributed in Wuyu Island, and A. dumbea is widely distributed in Baiha Reef, Qingyu Island, Wuyu Island, and Xiaobai Island. In this paper, the geographical distribution and the habits of 18 species of Astrogorgia are summarized, and the evolution of family and genus classification of Astrogorgia is discussed. The results enrich the geographical distribution information and coral species diversity records of Astrogorgia in China.

Assessing diversity of King Crab Lithodes spp. in the south-eastern pacific using phylogeny and molecular species delimitation methods

The purpose of this study was to test the hypothesis that the genetic diversity of commercially significant species of King Crabs (Lithodes spp.) along the south-eastern Pacific (SEP) comprises different independent evolutionary units (IEUs) with spatially isolated distribution. Nine localities from inner and open waters along the SEP Chilean coast (39°S-55°S) were sampled. We analyzed sequences from 173 individuals for the mitochondrial gene Cytochrome oxidase I (COX-I), 151 individuals for the Internal Transcribed Spacer 1 (ITS) and 135 for the structural ribosomal RNA (28S). Genetic delimitation was performed through three analytical methods: ABGD, GMYC, and its Bayesian implementation, bGMYC. Bayesian phylogenetic analyses and haplotype networks were also performed. Divergence time between clades was assessed for the COX-I marker and estimated from known evolutionary rates for this marker in other crustacean species and fossil calibration from other Anomuran species. Delimitation analyses, phylogenetic analyses, and mitochondrial haplotype networks suggested the presence of two deeply divergent mitochondrial lineages of Lithodes in the SEP, referred to as Clade1 and Clade 2. Nuclear markers showed low phylogenetic resolution and therefore were unsuitable for molecular species delimitation. Divergence time analysis of the mitochondrial lineages suggests a separation between Clades of approximately 2.3 Mya. The divergence time obtained suggested that Pliocene glaciations and deglaciations cycles could be involved in hybridization events between Lithodes IEUs at southern tip of South American coasts. The different frequencies of Lithodes haplotypes in inner and open water environments along SEP coasts could be explained by events such as the last glacial maximum or by differences in the adaptation of each clade to different environments. These findings support the necessity of evaluating the taxonomic status of Lithodes individuals found along SEP coasts under an integrative taxonomy approach or through markers with other evolution rates than those already used.

Phylogenetic assessment of the Metamasius hemipterus species complex (Coleoptera, Curculionidae, Dryophthorinae)

Metamasius is a large genus of dryophthorine weevils, with nearly 85 species. Among the economically important pests in the genus, M. hemipterus is currently separated in three subspecies, based largely on color patterns of the elytra, pronotum, and sternum. The tenuous limits of M. hemipterus subspecies were created over fifty years ago and never tested under a phylogenetic framework. Here, for the first time, we address the M. hemipterus species boundaries applying a molecular approach. We constructed a reduced genome representation of a few species using restriction site-associated DNA sequencing (RADseq). Phylogenetic analysis using either a complete supermatrix or only SNPs revealed a clear separation of Metamasius species. We suggest that M. h. carbonarius syn. nov. and M. h. sericeus be treated as the same species, M. sericeus (Oliver) stat. n., and elevate M. h. hemipterus as a separate species M. hemipterus (Linnaeus). We updated Vaurie's identification key to reflect the new species status. This systematic reassessment reflects a more natural classification for these remarkable and economically significant weevils.

Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Troglomorphism-any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs-has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism (stygomorphism) in freshwater fish requires a sound understanding of the evolutionary relationships between surface and stygomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived stygomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (>95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also support the recognition of six major clusters of species congruent with the identified clades in ordination space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.16 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.

Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning

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.

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

Solving the Coral Species Delimitation Conundrum

Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence - morphology, breeding trials and molecular approaches - to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analyses yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species, but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BACKGROUND

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS

In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS

Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

PREMISE

Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here.

METHODS

The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups.

RESULTS

The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades.

CONCLUSIONS

The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.

Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected F_ST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill

Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury to these and other species, the restoration of which requires an in-depth understanding of the biology, ecology, and genetic diversity of each species. To support a larger population connectivity study of impacted octocorals in the GoMx, this study combined sequences of mtMutS and nuclear 28S rDNA to confirm the identity of Swiftia sea fans in the GoMx, compare these markers for different polyp colors in the GoMx and Atlantic, and examine the phylogeny of the genus. Two mtMutS haplotypes were identified, one seemingly endemic to the northern GoMx. Compared to other North Atlantic Swiftia, S. exserta, the type of the genus was found to be extremely divergent and distinct from the two other Swiftia at both loci, with strong evidence of polyphyly in the genus. This information refines our understanding of the geographical distribution of injured coral and highlights how little is known about MCEs. Substantial taxonomic revisions may be needed for several taxa injured by the DWH oil spill.

Phylogenomics of Porites from the Arabian Peninsula

The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.

Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae)

Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.

Species delimitation integrative approach reveals three new species in the Nemertopsis bivittata complex

The presence of cryptic species is fairly frequent in many invertebrate groups and even more so among invertebrates with simple morphology, such as nemerteans. Consequently, the use of molecular methods for species delimitation has become a needed tool to complement morphological analyses to better recognise such species. Nemertopsis bivittata is one example of species with subtle morphological variation, but ample geographic distribution, being a good candidate for a species complex study. Here we applied two mitochondrial genes, and 2903 single nucleotide polymorphism (SNP) variants in addition to morphological characters to investigate the presence of cryptic species among specimens previously identified as N. bivittata along the Brazilian Coast. To do so, specimens were collected at 15 different sites in the north-east, south-east and southern regions. Three new species of Nemertopsis are described based on morphological and molecular analyses: Nemertopsis caete sp. nov., Nemertopsis pamelaroeae sp. nov. and Nemertopsis berthalutzae sp. nov. The species N. pamelaroeae and N. berthalutzae present broad distributions from north-east to south-east; N. caete, however, is restricted to the north-east coast. This is the first study to use this combined approach in nemerteans and shows the advantages of integrating genomic markers with classical taxonomy, and applying objective approaches to delimiting species as independently evolving entities.

Host shifting and host sharing in a genus of specialist flies diversifying alongside their sunflower hosts

Congeneric parasites are unlikely to specialize on the same tissues of the same host species, likely because of strong multifarious selection against niche overlap. Exceptions where >1 congeneric species use the same tissues reveal important insights into ecological factors underlying the origins and maintenance of diversity. Larvae of sunflower maggot flies in the genus Strauzia feed on plants in the family Asteraceae. Although Strauzia tend to be host specialists, some species specialize on the same hosts. To resolve the origins of host sharing among these specialist flies, we used reduced representation genomic sequencing to infer the first multilocus phylogeny of genus Strauzia. Our results show that Helianthus tuberosus and Helianthus grosseserratus each host three different Strauzia species and that the flies co-occurring on a host are not one another's closest relatives. Though this pattern implies that host sharing is most likely the result of host shifts, these may not all be host shifts in the conventional sense of an insect moving onto an entirely new plant. Many hosts of Strauzia belong to a clade of perennial sunflowers that arose 1-2 MYA and are noted for frequent introgression and hybrid speciation events. Our divergence time estimates for all of the Helianthus-associated Strauzia are within this same time window (<1 MYA), suggesting that rapid and recent adaptive introgression and speciation in Helianthus may have instigated the diversification of Strauzia, with some flies converging upon a single plant host after their respective ancestral host plants hybridized to form a new sunflower species.

Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny

Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

Lineage Identification Affects Estimates of Evolutionary Mode in Marine Snails

In order to study evolutionary pattern and process, we need to be able to accurately identify species and the evolutionary lineages from which they are derived. Determining the concordance between genetic and morphological variation of living populations, and then directly comparing extant and fossil morphological data, provides a robust approach for improving our identification of lineages through time. We investigate genetic and shell morphological variation in extant species of Penion marine snails from New Zealand, and extend this analysis into deep time using fossils. We find that genetic and morphological variation identify similar patterns and support most currently recognized extant species. However, some taxonomic over-splitting is detected due to shell size being a poor trait for species delimitation, and we identify incorrect assignment of some fossil specimens. We infer that a single evolutionary lineage (Penion sulcatus) has existed for 22 myr, with most aspects of shell shape and shell size evolving under a random walk. However, by removing samples previously classified as the extinct species P. marwicki, we instead detect morphological stasis for one axis of shell shape variation. This result demonstrates how lineage identification can change our perception of evolutionary pattern and process. [Genotyping by sequencing; geometric morphometrics; morphological evolution; Neogastropoda; phenotype; speciation; stasis.].

Identification of Eukaryotic Microalgal Strains

Proper identification and documentation of microalgae is often lacking in publications of applied phycology, algal physiology and biochemistry. Identification of many eukaryotic microalgae can be very daunting to the non-specialist. We present a systematic process for identifying eukaryotic microalgae using morphological evidence and DNA sequence analysis. Our intent was to provide an identification method that could be used by non-taxonomists, but which is grounded in the current techniques used by algal taxonomists. Central to the identification is database searches with DNA sequences of appropriate loci. We provide usable criteria for identification at the genus or species level, depending on the availability of sequence data in curated databases and repositories. Particular attention is paid to dealing with possible misidentifications in DNA databases and utilizing current taxonomy.

Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.

New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.

Phylogenomics of the Mesoamerican alligator-lizard genera Abronia and Mesaspis (Anguidae: Gerrhonotinae) reveals multiple independent clades of arboreal and terrestrial species

Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa.

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae)

A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)

Background

Heliopora coerulea, the blue coral, is the octocoral characterized by its blue skeleton. Recently, two Heliopora species were delimited by DNA markers: HC-A and HC-B. To clarify the genomic divergence of these Heliopora species (HC-A and HC-B) from sympatric and allopatric populations in Okinawa, Japan, we used a high throughput reduced representation genomic DNA sequencing approach (ezRAD).

Results

We found 6742 biallelic SNPs shared among all target populations, which successfully distinguished the HC-A and HC-B species in both the sympatric and allopatric populations, with no evidence of hybridization between the two. In addition, we detected 410 fixed SNPs linking functional gene differences, including heat resilience and reproductive timing, between HC-A and HC-B.

Conclusions

We confirmed clear genomic divergence between Heliopora species and found possible genes related to stress-responses and reproduction, which may shed light on the speciation process and ecological divergence of coral species.

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

Background

Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation.

Methodology

We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared.

Results

P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs.

Conclusion

This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.

Genomic and Mitochondrial Data Identify Different Species Boundaries in Aposematically Polymorphic Eniclases Net-Winged Beetles (Coleoptera: Lycidae)

Species delineation is essential for any evolutionary and biodiversity research, and recent advances in genomic sequencing have made it possible to robustly define species boundaries and detect hidden diversity. Here, we studied 14 species of aposematically colored New Guinean Eniclases (Coleoptera: Lycidae) whose conventional morphology- and single-locus mtDNA-based taxonomy has been contentious. We analyzed mitochondrial and restriction site associated DNA fragments to obtain a phylogenetic hypothesis and compared relationships recovered by the RAD analysis with species limits based on other information. The results show the presence of cryptic diversity and common mitonuclear discordance when over 30% of individuals were incorrectly assigned to species if only mitogenomic markers were considered. Nuclear data falsified the species rank of one species and identified one earlier unrecognized lineage deserving species rank. Further, our analyses demonstrate a highly variable phenotypic differentiation, with several pairs of cryptic species standing in contrast with genetically close but phenotypically highly divergent lineages. We show that morphological and mitogenomic analyses produce reliable information for taxonomy in most cases. Nevertheless, the species boundaries among closely related species should be based on all lines of evidence, including nuclear markers.

Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora

Background

Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression.

Results

All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis.

Conclusions

Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1476-2) contains supplementary material, which is available to authorized users.

Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)

Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.

A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

BACKGROUND

Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.

RESULTS

Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.

CONCLUSIONS

A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.