Species Delimitation Models Research Articles

Species Delimitation of Argonauta Paralarvae Reveals an Extensive Morphological Variability in the Northern Humboldt Current System

Argonauts or paper nautiluses are pelagic octopod cephalopods with a cosmopolitan distribution in tropical and subtropical waters around the world. Unlike other species of octopus, these are characterized by the fact that the female has a shell that serves as the breeding chamber for the eggs. Over time, this structure has been used as a taxonomic diagnostic character, causing problems in the systematics of this genus, with around 50 synonymies reported. Only two species, Argonauta argo and A. nouryi, have been reported in the Northern Humboldt Current System; however, there is taxonomic uncertainty regarding these species, which is reflected in the paralarvae (the first stage of life after hatching). In the paralarvae, the chromatophore patterns are considered to be conservative and reliable taxonomic characteristics. The objective of this study is to demonstrate the extensive variability in the chromatophore arrangement of Argonauta paralarvae in the Northern Humboldt Current using DNA barcoding and five species delimitation models. Our results include up to 11 different paralarvae morphotypes according to the pattern of chromatophores (number and arrangement) and 2 shell morphotypes. Species delimitation methods divided the 13 Argonauta morphotypes into two consensus molecular taxonomic units (MOTUs), A. argo and A. nouryi. Additionally, the results revealed an extensive morphological variability in the paralarvae and female shells of A. nouryi, demonstrating the importance of molecular data in studies involving species with different life stages, especially when this extensive morphological variability obscures conventional analyses.

Vicariance and cryptic diversity revealed by molecular phylogenetic analyses of estuarine Gammarus species (Crustacea: Amphipoda) due to formation of the Labrador Current

The metapopulation of the estuarine species Gammarus tigrinus along the east coast of the United States has been hypothesised to represent two cryptic species divided biogeographically off the coast of North Carolina, USA. This divergence has been attributed to a strong temperature gradient created by the formation of the cold Labrador Current c. 3.0 million years ago. In addition, the northern phylogeographic clade of G. tigrinus has been demonstrated to be invasive in estuarine habitats across a large portion of northern Europe. Recent collections of G. tigrinus from Florida and Maryland, USA, allow for new approaches to test this hypothesis. Using the nuclear 18S and 28S rRNA, and mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, species delimitation models provide support that the genetic divergence of the northern and southern clades is equivalent to species level. In addition, molecular clock data demonstrate that this phylogeographic divergence coincides with the formation of the Labrador Current. Furthermore, the collections of G. daiberi from Florida, a species with biogeographical and ecological characteristics similar to those of G. tigrinus, provide independent support for the hypothesis. The potential for invasive species to be cryptic highlights the need for accurate identification of taxa to ensure that appropriate biogeographical assessment of potential source populations and mechanisms of dispersal can be made.

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.

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 ‘forms’ in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.

Local-Scale DNA Barcoding of Afrotropical Hoverflies (Diptera: Syrphidae): A Case Study of the Eastern Free State of South Africa.

The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14-17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses.

Molecular and morphological evidence reveals the presence of the tadpole shrimp Lepidurus cf. couesii (crustacea: Branchiopoda) in Iran

Lepidurus couesii is a large freshwater branchiopod that is distributed broadly around the world. In this study, we used molecular and morphological methods to identify and record Lepidurus cf. couesii for the first time in Iran. The Almalou Gul specimens presented the characteristic number of rings, mediodorsal spines on the supra-anal plate, and the sulcus spines of the species L. couesii. A complete morphological characterization of the species and a comparison with previous records of Lepidurus apus in Iran is included in this work. Phylogenetic analysis based on the COI gene recovered the Iranian specimens as an independent lineage within the L. couesii species complex. The GMYC and the ASAP species delimitation models calculated at least four independent lineages within the L. couesii species-complex, some of them with probably restricted distributions. This study stresses –once again– the presence of several species-complexes within this group of crustaceans and the necessity to include molecular phylogenetic research to recognize the specific occurrence of different lineages within the genus Lepidurus.

New Insight into the Genus Cladocroce (Porifera, Demospongiae) Based on Morphological and Molecular Data, with the Description of Two New Species

During scientific expeditions in Indonesia and Vietnam, several sponge specimens belonging to the genus Cladocroce were collected. The integration of morphological and molecular analyses, incorporating species delimitation models (ABGD, ASAP, and bPTP) and phylogenetic approaches using three molecular markers (COI, 28S, and 18S–ITS1–5.8S–ITS2–28S), allowed us to discriminate three congeneric species. Two of these species (C. burapha and C. pansinii sp. nov.) were supported by morphological and molecular data, whereas a third species (C. lamellata sp. nov.) was delimited by morphological data only. We formally describe two new species, C. pansinii sp. nov. and C. lamellata sp. nov. C. aculeata is a newly recorded species for Indonesia and the first documented finding after the original description. The re-examination of the type material of C. burapha, and indirectly the molecular approach, allowed us to confirm that C. burapha lives in sympatry with C. pansinii sp. nov. in Vietnam and with C. lamellata in Indonesia. Thanks to these findings, we relocated the paratype of C. burapha to the new species described here, i.e., C. pansinii sp. nov.

Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS.

Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.

DNA Barcoding Confirms the Bluntnose Lizardfish, Trachinocephalus trachinus (Temminck and Schlegel 1846) (Aulopiformes: Synodontidae), in the Iranian Waters of the Gulf of Oman and the Existence of Cryptic Species Within Trachinocephalus

The first record of the Bluntnose lizardfish, Trachinocephalus trachinus (Temminck and Schlegel 1846) is confirmed by morphological and molecular (CO1 gene sequence) characters from the Iranian coast of the Gulf of Oman. All morphometric and meristic characters including snout length, eye diameter, body depth, Number of pectoral fin rays, lateral-line scales and dorsal fin rays, were concordant with characters of this species. In addition, identified CO1 haplotypes appeared in a monophyletic group with other haplotypes of Trachinocephalus trachinus in clade I, where all haplotypes of T. trachinus appeared in three species group based on two Species delimitation models (ABGD; PTP) in the phylogenetic tree. Interspecific distance appeared in the range of 0.04- 0.18, while intra-species was 0.0–0.1 (p-distance). The subject record is a new addition to the ichthyofauna of the northern Gulf of Oman, and also regarding the appearance of several cryptic species indicates the necessity of more integrative taxonomic studies in the Trachinocephalus group.

Integrated taxonomy reveals new threatened freshwater mussels (Bivalvia: Hyriidae: Westralunio) from southwestern Australia

The freshwater mussel Westralunio carteri (Iredale, 1934) has long been considered the sole Westralunio species in Australia, limited to the Southwest and listed as vulnerable on the IUCN Red List and under Australian legislation. Here, we used species delimitation models based on COI mtDNA sequences to confirm existence of three evolutionarily significant units (ESUs) within this taxon and conducted morphometric analyses to investigate whether shell shape differed significantly among these ESUs. “W. carteri” I was found to be significantly larger and more elongated than “W. carteri” II and “W. carteri” II + III combined, but not different from “W. carteri” III alone. We recognise and redescribe “W. carteri” I as Westralunio carteri (Iredale, 1934) from western coastal drainages and describe “W. carteri” II and “W. carteri” III as Westralunio inbisi sp. nov. from southern and lower southwestern drainages. Two subspecies are further delineated: “W. carteri” II is formally described as Westralunio inbisi inbisi subsp. nov. from southern coastal drainages, and “W. carteri” III as Westralunio inbisi meridiemus subsp. nov. from the southwestern corner. Because this study profoundly compresses the range of Westralunio carteri northward and introduces additional southern and southwestern taxa with restricted distributions, new threatened species nominations are necessary.

Cryptic species diversity in a widespread neotropical tree genus: The case of Cedrela odorata.

Reconciling the use of taxonomy to partition morphological variation and describe genetic divergence within and among closely related species is a persistent challenge in phylogenetics. We reconstructed phylogenetic relationships among Cedrela odorata (Meliaceae) and five closely allied species to test the genetic basis for the current model of species delimitation in this economically valuable and threatened genus. We prepared a nuclear species tree with the program SNPhylo and 16,000 single-nucleotide polymorphisms from 168 Cedrela specimens. Based on clades present and ancestral patterns ADMIXTURE, we designed nine species delimitation models and compared each model to current taxonomy with Bayes factor delimitation. Timing of major lineage divergences was estimated with the program SNAPP. The resulting analysis revealed that modern C. odorata evolved from two genetically distinct ancestral sources. All species delimitation models tested better fit the data than the model representing current taxonomic delimitation. Models with the greatest marginal likelihoods separated Mesoamerican C. odorata and South American C. odorata into two species and lumped C. angustifolia and C. montana as a single species. We estimated that Cedrela diversified in South America within the last 19 million years following one or more dispersal events from Mesoamerican lineages. Our analyses show that the present taxonomic understanding within the genus obscures divergent lineages in C. odorata due in part to morphological differentiation and taxonomic distinctions that are not predictably associated with genetic divergence. A more accurate application of taxonomy to C. odorata and related species may aid in its conservation, management, and restoration efforts.

Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola).

Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.].

Gorgoniapolynoe caeciliae revisited: The discovery of new species and molecular connectivity in deep-sea commensal polynoids from the Central Atlantic

Gorgoniapolynoe caeciliae (Fauvel, 1913) is a deep-sea commensal polynoid that lives in association with several genera of octocorals from the order Alcyonacea. The species has been recorded in the Caribbean and in both Atlantic and Indian Ocean basins. The wide geographic range of G. caeciliae, coupled with it having multiple host coral species and the evolution of its taxonomic description, hints that it could potentially be a species complex. This study investigated the morphological and genetic differentiation in 82 specimens of G. cf. caeciliae, sampled from four seamounts in the Central Atlantic separated by thousands of kilometres. Our combined morphological and molecular analyses, including species delimitation models (ABGD and bPTP) using COI and a phylogenetic approach using four molecular markers (COI, 16S, 28S, and 18S), agreed in identifying three distinct species; two supported by morphological and molecular data and a third species, using molecular data only, from the Indian Ocean which had been previously identified as G. caeciliae. We formally describe a new species in the genus, Gorgoniapolynoe pseudocaecliae sp. nov., the most common taxa found in our study. Our morphological analyses of some members of the genus Gorgoniapolynoe revealed the presence of elytra with possible photocytes (bioluminescent cells) and conspicuous macropapillae with long cilia emerging from them, whose function is discussed here. Our demographic analysis using COI for two Gorgoniapolynoe sp. detected a high potential for dispersal for G. pseudocaecliae sp. nov., with sites approximately 3000 km apart being well connected. Unusually there was also no genetic differentiation across their bathymetric range of over 1500 m. All in all, our study highlights the importance of applying integrative taxonomy to poorly studied deep-sea species.

Discovery of the male of Loxaulus hyalinus, and implications for the sympatric species Loxaulus laeta (Hymenoptera: Cynipidae: Cynipini): an integrative taxonomical case of species delimitation

ABSTRACT Loxaulus hyalinus Pujade-Villar & Melika, 2014 was originally described as an asexual form but the recent collection of male samples confirms that it is, actually, a sexual form. The male of L. hyalinus is here morphologically described. With L. hyalinus being a sexual form, the reasonable question arises whether it may be the alternate generation of the only other Loxaulus species currently known from Mexico, L. laeta Pujade-Villar, 2014 (asex). An analysis of the phylogenetic relationships between L. hyalinus (sex) and L. laeta (asex) shows an uncorrected genetic distance variation between sympatric and allopatric individuals averaging 6.4% (range 5.9–6.9%) between the two species independently of the sampled locality. Four different species delimitation models – Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of the Poisson tree processes (bPTP), Bayesian Phylogenetics and Phylogeography (BPP), and Bayesian Factor Delimitation (BFD) – support the distinctiveness of the two Loxaulus species.

Phylogenetic analyses of a new freshwater amphipod reveal polyphyly within the Holarctic family Crangonyctidae, with revision of the genus Synurella

Abstract A new genus and species of crangonyctid amphipod, Sicifera cahawba gen. & sp. nov., is described from Dallas County, AL, USA, based on both morphological and molecular comparison with similar crangonyctids. These data, with the application of four species delimitation models, identify the taxon as distinct when compared with related species. Nearctic members of the crangonyctid genus Synurella form a separate, well-supported monophyletic lineage when compared with Palaearctic members, which differ considerably in both molecular and morphological markers. Nearctic members, with the exception of the enigmatic Synurella (Eosynurella) johanseni, are placed in the newly erected Sicifera. The separation of these two genera implies that Palaearctic and Nearctic crangonyctid lineages might not be as closely related as once thought, and their evolutionary and biogeographical history requires further review. In addition, a key to Nearctic members of the genera Eosynurella/Sicifera is presented to aid in future identification.

Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi.

Species delimitation among closely related species is challenging because traditional phenotype‐based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high‐throughput sequencing, it has become increasingly cost‐effective to acquire genome‐scale data which can resolve previously ambiguous species boundaries. As the availability of genome‐scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro‐endemism in a lineage of lichen‐forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single‐locus and genome‐scale data consisting of (a) single‐locus species delimitation analysis using ASAP, (b) maximum likelihood‐based phylogenetic tree inference, (c) genome‐scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross‐validate results between genome‐scale and single‐locus datasets, differently sampled subsets of genomic data and to control for population‐level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro‐endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.

Resolving the Tetrastigma loheri s. l. Species Complex (Vitaceae) in the Philippines: No Evidence for Recognizing More than One Species

Abstract— Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forest ecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii, T. philippinense, T. stenophyllum, and T. trifoliolatum. This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines. For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leaf shape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable species when used for studying patterns of genetic diversity and connectivity in the Philippines.

Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation.

Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.

Species Delimitation of Southeast Pacific Angel Sharks (Squatina spp.) Reveals Hidden Diversity through DNA Barcoding

Angel sharks are distributed worldwide in tropical to subtropical waters. Across the Eastern Pacific Ocean (EPO), two valid species are reported: The Pacific angelshark Squatina californica and the Chilean angelshark Squatina armata; however, there is still uncertainty about their geographic distribution, mainly along the northern Peru coast where the species have been reported to be sympatric. The aim of this study is to describe the genetic differences between the genus Squatina from the EPO, including samples from northern Peru, and using DNA barcoding and three species delimitation models: Poisson tree processes (PTP) model, Bayesian implementation of the PTP (bPTP) model and the general mixed Yule coalescent (GMYC) model. The three approaches summarized 19 nominal Squatina species in 23 consensus Molecular Taxonomic Units (MOTU). Only 16 of them were in accordance with taxonomic identifications. From the EPO, four Squatina MOTUs were identified, one from North America (S. californica USA/Mexico) and three sampled in northern Peru, S. californica Peru, S. armata and Squatina sp. (a potential new species). This study contributes to the management and conservation policies of angel sharks in Peru, suggesting the presence of an undescribed species inhabiting the northern Peruvian coast. The use of molecular approaches, such as DNA barcoding, has the potential to quickly flag undescribed species in poorly studied regions, including the Southeast Pacific, within groups of ecologically and economically important groups like angel sharks.

Genetically diverse yet morphologically conserved: Hidden diversity revealed among Bornean geckos (Gekkonidae: Cyrtodactylus )

The appreciation of cryptic biological diversity, and the pace at which it is recognized, has greatly increased with the use of molecular systematic techniques. The gekkonid genus Cyrtodactylus Gray, 1827 is one example of a group that has undergone a particularly rapid increase in recognized diversity due to molecular systematic studies. Many of these new species result from recognizing closely related but diagnosable lineages into sister taxa. Our study implements a multi-faceted approach to delimit cryptic Cyrtodactylus lineages on the Southeast Asian island of Borneo using morphological, ecological, and multilocus genetic data. We use multiple species delimitation models to assess species boundaries and identify clades that warrant further investigation. Unlike most morphologically cryptic species that have recently diverged, we find evidence of cryptic lineages being polyphyletic. Using multivariate statistical analyses, we show minimal phenotypic distinction between putative cryptic species within the C. pubisulcus complex. Despite not finding morphologically diagnostic characters, we demonstrate strong evidence for the specific recognition of C. hantu sp. nov. and C. miriensis sp. nov., which are currently considered conspecific with C. pubisulcus, from Sarawak, Malaysia. Our new concept for C. pubisulcus restricts the geographic range of the species to specific regions in western Sarawak, Malaysia, thus underscoring the need to conserve the limited remaining habitats of these species, as well as the considerable undescribed diversity across Borneo.