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Oceanic islands are hotspots of marine biodiversity, and biogeographic and evolutionary studies can provide important knowledge about the origin and diversification of the species that inhabit them. In the South Pacific, the Juan Fernández Archipelago (JFA) stands out for its high endemic biota, most of them endangered by human activities. Currently, two octopus species are recognized in JFA, but their taxonomic identity is not conclusive. In the present study, we performed morphometric and molecular analyses of both species inhabiting the JFA and contrast them with other species worldwide. Morphological, phylogenetic analysis, genetic diversity, and divergence times between species were estimated. Morphometric analysis did not show significant differences in body shape of males between/within Octopus species from JFA, only between females from different localities. However, phylogenetic and species delimitation analyses support the presence of two species in the JFA, namely Octopus mimus and Octopus vulgaris. In addition, both species show evidence of different divergence and colonization histories into the JFA during the Pleistocene. These findings do not only shed light on the identity, origin, and colonization time of the species, but also provide the basis to generate informed decisions on management and conservation. The recent colonization time and low genetic diversity observed in both species suggest that these populations are vulnerable to drastic changes, such as those caused by anthropic effects. [ABSTRACT FROM AUTHOR]

Phylogeographic studies on widespread rainforest species from West and Central Africa often reveal genetic discontinuities. These discontinuities can originate from past barriers to gene flow resulting from long-lasting population fragmentation during glacial periods, according to the forest refuge hypothesis. This study 69 nuclear SNPs, 13 plastid SNPs, and 24 mitochondrial SNPs to characterized the distribution of genetic diversity in 377 individuals of the widespread tropical tree Khaya ivorensis, in western and central African evergreen forests. Two very well-differentiated nuclear genetic clusters (FST = 0.28) are located respectively in West and Central Africa. The gradual transition of allele frequencies between the clusters across a broad geographic area going from Cameroon to Nigeria accords with the recognition of a single species, although we show an incipient divergence that could eventually lead to the separation of two taxa. The two clusters have similar genetic diversity at nuclear SNPs. However, the cytoplasmic data revealed high haplotypic diversity and numerous endemic haplotypes in Central Africa, and only one widespread haplotype in West Africa, suggesting an ancient colonization of West Africa from Central Africa. The genetic diversity inside and outside putative forest refugia (Anhuf et al., Palaeogeogr Palaeoclimatol Palaeoecol 239:510–527, 2006) does not differ significantly in either genetic cluster. Hence, we cannot confirm that forest refugia played a particular role in the pattern of distribution of genetic diversity in K. ivorensis. Owing to the high haplotypic diversity of their populations, Central Africa, especially Gabon, constitutes a priority area for the conservation of the genetic diversity of K. ivorensis. [ABSTRACT FROM AUTHOR]

Species are fundamental biological units and can be treated as testable scientific hypotheses. Historically, species in the genus Coccoloba have been published based only on classical morphology. One of these species, Coccoloba laevis, contains many specimens with strong morphological differences. We here test the hypothesis that these morphological variations are consistent with the circumscription of C. laevis as a single taxonomic entity. In addition to classical morphology, we used linear morphometry, vascular anatomy, and potential geographic distribution to delineate a distinctive morphotype of C. laevis from the remainder of C. laevis s.s. Statistical analysis showed significant differences for all ten morphometric variables. Petiole and midrib anatomy also pointed to differences in both shape and arrangement of vascular bundles between the distinctive morphotype and the remainder of C. laevis s.s. The potential distribution model yielded a wide distribution for C. laevis s.s. in the coastal zone of northeastern Brazil. The distinctive morphotype, however, had a contiguous and restricted distribution within this range. Based on our results, we here reestablish Coccoloba candolleana at the species level, which has been previously treated as a synonym of C. laevis. Both species differ morphologically mainly by habit, and the shape and size of ochrea, leaf, petiole, inflorescence, pedicel, and fruit. Because of its restricted distribution in a coastal ecosystem associated with strong anthropogenic disturbance, we consider C. candolleana as endangered. [ABSTRACT FROM AUTHOR]

The genus Gracilinanus ranges from savannas to dense forests in South America, yet its systematics have never been thoroughly investigated across its wide distributional range. We assessed Gracilinanus phylogenetic relationships, species boundaries, and geographical limits using mtDNA sequences. Our analysis confirmed the distinctiveness of the six recognized species (G. aceramarcae, G. agilis, G. emiliae, G. marica, G. microtarsus, and G. peruanus), with a mean p-distance for interspecific nucleotide sequence divergences ranging from 13–16.2% and robust phylogenetic support (BPP > 0.95; BS > 75%). Refined species delimitation approaches (GMYC, PTP, ASAP) revealed potential cryptic diversity, suggesting up to 20 candidate species. Three geographically structured and divergent lineages (4.1–4.8% sequence divergence) were identified within G. agilis, extending its Cerrado range. Within G. emiliae, we found divergence values ranging from 4.7–5.7% and the first known record for the northeastern Atlantic Forest. Three divergent clades were recovered within G. microtarsus (9.0–9.8% sequence divergence), including a new lineage for the northern Atlantic Forest. For G. peruanus, we found two divergent lineages (7.2%) and the first documented occurrence for Amazonian lowland forest. This comprehensive sampling revealed greater genetic diversity in Gracilinanus, extending its geographic limits. Here we propose nine putative new species, emphasizing a hidden diversity that warrants formal description and further increases the taxonomic diversity of this genus. These newly identified lineages underscore the urgency of inventorying and conserving the threatened ecosystems of the Cerrado and Atlantic Forest hotspots. [ABSTRACT FROM AUTHOR]

Life history characteristics of cryptobenthic reef fishes (CRFs), such as their fast growth and reproductive rates, near-shore larval retention and high turnover, predispose these species to rapid diversification and cryptic speciation. This may be particularly true for isolated CRF populations. The sailfin blenny, Emblemaria pandionis, is widespread throughout the Caribbean and is found on the reefs of the Flower Garden Banks, an isolated reef system in the NW Gulf of Mexico. Using DNA barcoding and multi-locus delimitation, we show that E. pandionis is a species complex comprised of at least four distinct taxonomic units in the Caribbean, one at the Flower Garden Banks, a second in eastern Florida, a third in the central Caribbean and a fourth in Curaçao. The phylogenetic relationships within the E. pandionis species complex are defined by well-established phylogeographic barriers to gene flow in the Caribbean. Populations of E. pandionis from eastern Florida are genetically distinct from populations found in the Bahamas, highlighting the role of the Florida Strait as a strong barrier to gene flow and populations in Curaçao are deeply divergent from all other populations sampled in the Caribbean. Results from this study highlight the roles of isolated reefs and ocean currents in the speciation of cryptobenthic reef fishes. [ABSTRACT FROM AUTHOR]

Background: Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set. Results: Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes. Conclusions: The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis. [ABSTRACT FROM AUTHOR]

DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys. [ABSTRACT FROM AUTHOR]

Cephalopod fisheries are increasing, but little is known about the cryptic diversity of some key commercial species. Recent studies have shown that cryptic speciation is common in cephalopods, including several oceanic squids formerly considered 'cosmopolitan species.' Further efforts are needed to investigate the cryptic diversity of commercial species, to inform management and support sustainable fisheries practices. Thysanoteuthis rhombus is an oceanic squid, currently recognized as the single species of the family Thysanoteuthidae. Thysanoteuthis. rhombus has a global distribution in tropical and subtropical waters and is an economically important species, with the highest catches occurring off Okinawa in Japan and of potential fishery resource for other countries due to its high abundance and large size. Here, we used sequences from 12S rRNA, 16S rRNA, and cytochrome c oxidase I to characterize its cryptic diversity using samples collected throughout most of its known geographic range. We identified three different putative species whose distributions are concordant with main ocean basins: Thysanoteuthis major, the most abundant species, is widely distributed in the North Pacific Ocean, North Indian Ocean, and limits of the South Atlantic Ocean; Thysanoteuthis rhombus is distributed in the North and South Atlantic Ocean and Mediterranean Sea; and Thysanoteuthis cf. filiferum, likely the least sampled to date, is found in the southwestern Pacific Ocean. A sister relationship was observed between T. rhombus and T. major, and T. cf. filiferum was found to be the most divergent species. Based on our divergence estimation, we hypothesize that the closure of the Isthmus of Panama during the early Pliocene played a significant role in the split of T. rhombus and T. major, while the split of their ancestor from T. cf. filiferum coincided with an increase in the Pacific Walker Circulation and the longitudinal gradient of surface temperatures in the Pacific Ocean during the Late Oligocene and Early Miocene. Our work identifies three different putative species within Thysanoteuthis and has potential use for improving fishery management and conserving the diversity in these species. [ABSTRACT FROM AUTHOR]

The widespread Tantilla melanocephala is a South American snake, which has a convoluted taxonomic history and a poorly addressed systematics. The taxonomic identity and the phylogenetic affinities of their populations are unclear, suggesting the existence of a complex of undescribed species. Here, we preliminarily address the morphological diversity and genetic structure of the T. melanocephala complex through comparative morphological approaches and phylogenetic analyses using maximum likelihood. Our results confirm the presence of hidden diversity within the T. melanocephala complex and strongly indicate that the populations of T. melanocephala from southern South America represent a distinct lineage, which is morphologically diagnosable under a unique combination of character states. Therefore, we formally describe these populations as a new species and present a comparison among all other South American species of Tantilla. We also estimate the divergence times of the main clades within the complex through Bayesian analysis, suggesting a biogeographical scenario of lineage diversification. Finally, our study clarifies aspects of the intricate taxonomy of the T. melanocephala complex, providing a framework for future studies to avoid the description of synonyms. [ABSTRACT FROM AUTHOR]

This study was designed to assess whether or not existed interspecific hybrids between the two lesser known African taxa in Solanum Merolloids section Solanum; S. tardremotum and S. florulentum that confused their taxonomy. Hybridization is one of the factors that blur boundary between closely related species. It is an indication that there is semi-permeable boundary through which genes are flowing across. In the African species of section Solanum it has been hypothesized that interspecific hybridization is one of the factors complicating the delimitation of species though this claim has never been examined systematically. Solanum tarderemotum and S. florulentum were all described by Bitter from Tanzania. Through history the two taxa have been considered separate species, different species mixed with hybrids and recently the boundary of S. tarderemotum has been expanded to include S. florulentum s. str. and materials thought to be hybrids. DNA was isolated from 63 individuals belonging to 22 accessions and two amplified fragment length polymorphism (AFLP) primer combinations; EcoRI + AAC/MseI + CAC and EcoRI + ACC/MseI + CAT used. Clustering used PAST software. Five clusters were generated, S. tarderemotum s. str. and S. florulentum s. str., fell in different clusters. The two taxa shared only 41% of their bands which was less that what was shared between them and their supposed hybrids in two of the three remaining clusters. Some individuals from certain accessions segregated in different clusters. Intermediary and segregation indicates exists hybrids in midst of good species S. tarderemotum and S. florulentum and this could be the reason of the confused species delimitation. [ABSTRACT FROM AUTHOR]

Mushrooms are important organisms because of their human nutritional and medicinal value. With the expansion of the cultivation of edible mushrooms, fungal diseases have become a major problem in limiting their production. Numerous fungi can cause mushroom deformation or rots. In this publication we report on fungal diseases found during Morchella cultivation in China, with emphasis on morphology and phylogeny to characterise species. The key findings include 1) establishment of a new family Albomorchellophilaceae in Hypocreales, and a novel monotypic genus Albomorchellophila with the type species A. morchellae. Divergence time estimates indicate that Albomorchellophilaceae diverged from its sister family Calcarisporiaceae at ca. 105 (92–120) MYA; 2) the phylogeny and morphology of the family Pseudodiploosporeaceae (Hypocreales) is revised. The family contains a single genus Pseudodiploospora. Intraspecific genetic analyses of Pseudodiploospora longispora reveals significant base differences within strains, especially in the regions of protein-coding genes RPB 2 and TEF; 3) four fungicolous taxa, i.e., Cylindrodendrum alicantinum, Hypomyces aurantius, Hypomyces rosellus, and Trichothecium roseum, are reported as putative pathogens on cultivated morels for the first time. In addition, the previously reported pathogens of morels, Clonostachys rosea, Clonostachys solani, Hypomyces odoratus, and Pseudodiploospora longispora are also detailed in their symptoms and morphology; 4) the phylogeny and morphology of "Zelopaecilomyces" previously placed within Pseudodiploosporeaceae are re-assessed. "Zelopaecilomyces" is proved to be introduced through a chimerism of gene fragments sourced from two distinct organisms. Consequently, it is recommended that "Zelopaecilomyces" should not be recognised due to the mixed up molecular data in phylogeny and a lack of support from morphological evidence. Furthermore, this study discusses the voucher specimen Paecilomyces penicillatus (CBS 448.69), which may contain two mixed taxa, i.e., Pseudodiploospora longispora and a member of Penicillium. Publications on pathogenic fungi of cultivated mushrooms is sporadically, which leads to a lack of understanding of causal agents. As a follow up to the diseases of morel cultivation, we also review the fungal diseases of cultivated mushrooms reported over the last four decades. More than 130 pathogens affect the growth and development of the main cultivated mushrooms. The taxonomic diversity of these pathogens is high, distributed in 58 genera, 40 families, 20 orders, 12 classes and six phyla. The host infected are from Ascomycota to Basidiomycota, mainly being reported from Agaricus bisporus, Cordyceps militaris, Morchella spp., and Pleurotus spp. This study not only enriches our current knowledge on the diversity of pathogens of cultivated mushrooms, especially morels, but also recognizes the importance of some taxa as potential pathogens. Taxonomic investigation and accurate identification are initial and key steps to understanding pathogen-mushroom interactions, and will result in better disease management strategies in the mushroom industry. [ABSTRACT FROM AUTHOR]

Polychaetes are annelids predominantly marine and constitute an important part of marine communities. The genus Alitta, of the family Nereididae, comprises nine recognized species, including Alitta succinea, considered cosmopolitan. The species was first described from the Helgoland (Germany) and has been recorded on the Brazilian coast. However, evidence suggests that A. succinea might be a complex of cryptic species. The aim of this short communication is molecularly analyzing specimens of Alitta succinea to ascertain the status of the species in Brazil. The study encompassed molecular analyses of COI and 16S sequences using data obtained from eight specimens collected from three localities at Rio de Janeiro and seven specimens collected from Santa Catarina, in addition to available data from GenBank and BOLD Systems. Molecular analyses clustered specimens from Brazil, the type locality and other localities in the same clade, reinforcing the status of A. succinea as an invasive species. However, additional studies, including more extensive molecular and morphological analyses, are necessary to clarify the distribution of the Alitta succinea along the Brazilian coast. [ABSTRACT FROM AUTHOR]

Traditionally, the apparent paucity of biogeographic barriers in marine environments when compared to terrestrial and freshwater habitats has been associated with high gene flow rates among geographically distant populations. However, physical traits such as tide currents, temperature, and salinity levels may serve as ecological boundaries thus leading to restricted-range phylogeographic patterns (e.g., the outflow plume from the Amazonas-Orinoco rivers between the Caribbean and the Brazilian Province) according to adaptive features of coastal organisms. To assess the degree of cohesiveness among populations and species of marine and estuarine fishes along a latitudinal gradient from Western South Atlantic, we carried out comparative phylogenetic and species delimitation analyses based on Cytochrome C Oxidase I (COI) sequences of 34 fish taxa from the Caribbean and Brazilian coasts. Distinct values of genetic diversity were revealed for both Provinces, ranging from moderate (1 to 2%) to high (≥ 2%) in 11.76% and 20.59% of the analyzed taxa, respectively. Furthermore, a significant genetic differentiation was observed within the nominal taxa Diapterus auratus, Citharichthys spilopterus, and Scorpaena plumieri from the Caribbean, as well as for Haemulon plumierii between the Caribbean and Brazilian Provinces. Such divergence is likely to result from temporal isolation among local populations during sea-level fluctuations during the Pliocene-Pleistocene period. The present findings demonstrate that similar biogeographic boundaries may result in species-specific patterns of genetic connectivity, possibly associated with ecological constraints. Since molecular operational taxonomic units (MOTUs) were identified in certain formal taxa from both Provinces, a systematic revision of these groups is highly recommended. At last, multispecies COI data proved to be helpful to phylogeographic inferences and to support appropriate policies for the conservation of natural resources. [ABSTRACT FROM AUTHOR]

Background: In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data. Objective: Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae). Methods: Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed. Results: The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively. Conclusion: Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors. [ABSTRACT FROM AUTHOR]

The advent of molecular techniques has resulted in the discovery of previously unknown cryptic species in many organisms, including rotifers, allowing researchers to perform detailed tests on reproductive barriers between closely related taxa. Here, we review the available literature about molecular techniques implemented for detecting cryptic diversity in rotifers and delimiting species, and discuss the potential mechanisms of reproductive isolation among rotifer cryptic species. Half of the evaluated studies used quantitative statistical approaches for species delimitation. Species boundaries defined by molecular approaches were also examined by conducting mating experiments. Those mating experiments were used to test various reproductive barriers. Most (75%) studies that identified reproductive isolation mechanisms provided evidence of prezygotic barriers. The available literatures suggest that behavioral reproductive isolation may have a more important role than other prezygotic barriers in facilitating reproductive isolation. Postzygotic barriers such as hybrid unviability or sterility and female mortality also contribute to reproductive isolation among rotifer cryptic species. The prevalence of prezygotic barriers in our assessment may stem from the difficulty of studying postzygotic barriers, which can require long-term maintaining and monitoring of rotifer populations. Sequencing tools, including whole genome sequencing, could be implemented to investigate the molecular basis of reproductive isolation in rotifers. [ABSTRACT FROM AUTHOR]

The inability to precisely identify biological species has direct impacts on conservation efforts, which is especially true among taxa of great commercial interest such as representatives of the Penaeini tribe. Those shrimp supply more than half of the global demand for crustaceans and have important functional roles in ocean ecosystems. Recent systematic studies suggest that the diversity of taxa within Penaeini is underestimated, and there are controversial taxonomic classifications. In this work, we used phylogenetic and phylogeographic approaches to assess the genetic diversity and evolutionary of representatives of the Penaeini tribe, focusing on the mitochondrial cytochrome oxidase subunit I gene. A total of 1680 COI sequences from 24 species were accessed on the Bold Systems platform. We detected several identification errors and synonyms among the 15 taxa of the tribe, principally within the genus Penaeus. Phylogeographic analyses allowed the identification of highly structured populations within several ecoregions of the Atlantic (19), Indian (16), and Pacific (10) oceans. The delimitation methods (GMYC, bPTB, and BINs) suggest are cryptic species such as Fenneropenaeus indicus (2 MOTUs), Litopenaeus vannamei (2 MOTUs), Penaeus monodon (3 MOTUs), and P. semisulcatus (4 MOTUs). The highest cryptic diversity concentration was found in the Indo-West Pacific region, suggesting it as the center of origin for the tribe. Our data provide important information that could subsidize management actions and guarantee the long-term maintenance of those lineages and their stocks. [ABSTRACT FROM AUTHOR]

Color ontogeny and variations associated with discrete morphological differences may generate taxonomical challenges, which requires multiple data types and in-depth historical review. The nudibranch known as the Spanish dancer, Hexabranchus sanguineus, is a classic example with over 200 years of taxonomic confusion. Currently, H. sanguineus is accepted by most authors as a single species from the Indo-Pacific Ocean with Hexabranchus morsomus as a valid species from the Atlantic Ocean. Yet, despite these species being highly studied, their systematic status remains debatable. Over 30 synonyms have been proposed for H. sanguineus and even a distinct genus for H. morsomus. Here we provide, for the first time, a comprehensive review of all proposed names and an integrative taxonomic revision of the genus including morphological and molecular data. Our results reveal that H. sanguineus is a complex of five species: four previously described and an undescribed species, one of the largest nudibranchs in the world: Hexabranchus giganteus sp. nov. The genus Caribranchus is considered a junior synonym of Hexabranchus Ehrenberg, 1828 and the ontogeny of color pattern is discussed. [ABSTRACT FROM AUTHOR]

The white-eared opossum, Didelphis albiventris Lund, 1840, is one of the most widely distributed South American marsupials. As currently defined, the species ranges from northeastern and central Brazil through Paraguay and central Bolivia, all of Uruguay, and in Argentina, from the north to northern Patagonia. Previous phylogeographic analyses found two haplogroups, one corresponding to northeastern and central Brazil and the other to southern Brazil, Bolivia, and Paraguay. In those studies, differentiation was based on the geographic distance between both regions and the presence of geographic barriers among populations. The aims of the present contribution were to perform population-genetic analyses using the mitochondrial markers cytochrome c oxidase 1 (COI) and cytochrome b (cyt b) in order to elucidate the phylogeographic history of this species by incorporating samples from Argentina into the published datasets, and to evaluate whether there is more than one taxonomic entity under the name Didelphis albiventris. We studied the craniodental morphology of the species and used environmental niche modeling (ENM) as an additional methodology to investigate the environmental factors affecting its distribution. Our molecular, morphological, and ENM results strongly suggest the existence of two taxonomic entities under Didelphis albiventris, one in southern Brazil, Argentina, Paraguay, Uruguay, and Bolivia, and the other in central and northern Brazil. Data from specimens in the missing middle part of the taxon's range and evidence from nuclear markers are needed before formalizing a taxonomic split. [ABSTRACT FROM AUTHOR]

During a study of morphological variations in bent-wing bats (Miniopterus), we found that specimens originating from the Cao Bang province of Vietnam, identified as M. fuliginosus, were closer in size to the larger species, M. magnater. Mitochondrial gene analysis clearly places these specimens in the former species. At the same time, morphometric analysis of 21 cranial measurements definitely puts these specimens closer to M. magnater and shows their differences from M. fuliginosus samples from different parts of the species range. We assume that, in the low mountains of northern Vietnam and southern China, M. fuliginosus, due to as yet unknown circumstances, occupies the niche of a larger species. However insufficient data on nuclear markers also assume a hybrid origin of this population, with mtDNA introgression from another species. [ABSTRACT FROM AUTHOR]

Freshwater mussels are considered the most imperiled group of organisms in North America and systematics research has played an integral role in the development and implementation of their conservation. Despite the importance of systematics in conservation planning, the evolutionary relationships between many mussel taxa remain poorly explored, clearly illustrated by Strophitus undulatus. This species is wide-ranging, occurring in streams across the United States and Canada with a disjunct population in the Colorado River drainage in central Texas. The widespread distribution of S. undulatus, as well as high intraspecific morphological variation, has led previous authors to doubt the taxon is representative of a single species. In this study, we set out to investigate species boundaries in S. undulatus by integrating environmental, molecular, and morphological datasets. Molecular and morphological data supported S. undulatus from the Colorado River as distinct, which was supplemented by a species distribution modeling approach, suggesting potential adaptation to Edwards Plateau streams has contributed to speciation. Given our findings, we formally describe a new species of freshwater mussel, Strophitus howellsi, endemic to streams along the Edwards Plateau in the Colorado River drainage. A conservation assessment of S. howellsi suggests the species is extremely rare within a highly restricted distribution and may warrant future recovery actions. Our findings build on a growing body of literature highlighting aquatic endemism along the Edwards Plateau and have significant conservation implications for freshwater mussels in Texas. [ABSTRACT FROM AUTHOR]

Accurate species identification is a key component of biodiversity research. DNA barcoding is an effective molecular method used for fish species identification. We aimed to study the DNA barcoding of fish in Zhoushan coastal waters, explore the differences and applicability of two gene fragments (12S rRNA and COI) of DNA barcoding in fish species identification, and established a comprehensive fish barcoding reference database. Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding. A total of 264 12S rRNA sequences (belonging to eight orders, 31 families, 55 genera, and 66 species) and 188 COI sequences (belonging to seven orders, 30 families, 48 genera, and 58 species) were obtained. The lengths of the 12S rRNA sequences ranged from 165 to 178 bp, and the guanine-cytosine (GC) content was 45.37%. The average 12S rRNA interspecific and intraspecific genetic distances (K2P) were 0.10% and 26.66%, respectively. The length of the COI sequence ranged 574–655 bp, and the content of GC was 45.97%. The average 12S rRNA interspecific and intraspecific genetic distances (K2P) were 0.16% and 27.45%, respectively. The minimum interspecific genetic distances of 12S rRNA and COI (1.23% and 1.86%) were both greater than their maximum intraspecific genetic distances (2.42% and 8.66%). Three molecular analyses (NJ tree, ABGD, and GMYC) were performed to accurately identify and delineate species. Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method, and the delimitation results of ABGD and GMYC are consistent with the final species identification results. Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification, and 12S rRNA has good application prospects in the environmental DNA (eDNA) metabarcoding of marine fish. [ABSTRACT FROM AUTHOR]

Whereas most cnidarians are macrofaunal, a few microscopic lineages have evolved, and some of them inhabit marine sediments. The meiofaunal genus with the most species is Halammohydra, comprising nine nominal species. Species are described with high intraspecific variability in, e.g., the number of tentacles and statocysts and the shape and length of tentacles and body, complicating morphological identification to species level. Additionally, there is not much molecular data available. This study aims to revise already described species with morphological and molecular methods, as well as, to delineate potential new species answering questions about their geographical distribution. For this, specimens were sampled at 16 locations in the Northwest Atlantic and two localities in the East Atlantic, documented with light microscopy, and fixed individually for sequencing (16S, 18S, and CO1). Herewith, morphological characters were linked to a specific sequence, enabling the testing of character variation within one molecular phylogenetic group. Phylogenetic analyses were conducted (Bayesian Interference and Maximum Likelihood) in combination with species delimitation tests (ABGD, GMYC, and bPTP). Four already described species were identified in the data sets, and all of these were found at multiple localities. Four new species are described. Overall, the combined molecular and morphological data acquisition revealed multiple new species and a high degree of sympatry in Halammohydra. This, together with the confirmed excessive intraspecific variation in morphological traits, underlines the necessity of molecular sequencing for the taxonomy and species identification of Halammohydra. [ABSTRACT FROM AUTHOR]

The stabilized and the trailing edge glacial relicts are candidate model organisms to be used to link taxonomy to phylogeography. We attempted to establish such a link by considering the taxonomy and phylogeography of the genus Anterastes, consisting of glacial relict taxa/populations. Species delimitation tests indicated 13–22 candidate species in the genus. Analyses suggested inversely related genetic and phenotypic divergence. By integrating these results, we reached the following conclusions. (i) The plausible taxonomical composition is recognizing 16 species in the genus; of these three are new, A. kizkayasiensis sp. n., A. muratdagensis sp. n., and A. boreoanatoliensis sp. n., and the last two are cryptic. (ii) Generic radiation corresponds to three stages as Pliocene, Pleistocene prior to mid-Pleistocene Transition (MPT), and post-MPT. The ultimate ancestor of two species, corresponds to the first and of other 14 to the second and proximate ancestor of all species to the third period. These ages suggest that the pre-MPT ancestors are stabilized edge while those of post-MPT are trailing edge populations. (iii) Since members of the genus demand cold habitats, the isolated relict ancestors on highlands evolved under similar selection pressures, and this led to a conserved phenotype, consequently to cryptic or morphologically poorly diverged species, as genetic data indicate each constitutes a reproductively isolated distinct phylogenetic unit. (iv) Although morphological diagnosability is poor, each species fulfills criteria of several species concepts and can be differentiated by clear allopatric range, providing one of five criteria assumed by Darwin for species delimitation. [ABSTRACT FROM AUTHOR]

A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringlet Erebia manto, which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priorities. Using several thousand nuclear genomic markers, we evaluated to which degree the bubastis lineage from the Alps and the vogesiaca lineage from the Vosges, are genetically isolated from the widespread manto lineage. Our results suggest that both lineages are genetically as strongly differentiated from manto as other taxonomically well separated sibling species in this genus from each other, supporting a delineation of bubastis and vogesiaca as independent species. Given the restricted and isolated range of vogesiaca as well as the disjunct distribution of bubastis, our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes. [ABSTRACT FROM AUTHOR]

Documenting species and population diversity is becoming increasingly important as the destruction and degradation of natural ecosystems are leading to a worldwide biodiversity loss. Despite the rapid development of genetic tools, many species remain undocumented and little is known about the diversity of individuals and populations, especially for tropical African plants. In this study, we aim to identify putative hidden species and/or differentiated populations in the tropical African tree Staudtia kamerunensis Warb. (Myristicaceae), a widespread species characterized by a high morphological diversity and a complex taxonomical history. Historical herbarium vouchers were sampled and leaf or cambium samples were collected in the field, dried in silica gel, and subsequently genotyped at 14 microsatellite loci (SSRs), as well as sequenced for two nuclear genes (At103, Agt1) and one plastid region (psbA-trnH). These genetic data were then analyzed using Bayesian clustering, population genetics, and the construction of haplowebs to assess genetic clustering patterns, the distribution of genetic diversity, and genetic differentiation among populations. Multiple genetically differentiated clusters were observed in parapatry throughout Central Africa. Genetic diversity was high and similar among these clusters, apart from the most differentiated populations in southeast Democratic Republic of the Congo (DR Congo), which showed lower levels of genetic diversity. The genetic breaks detected between S. kamerunensis populations are likely not indicative of hidden species but rather result from ancient rainforest fragmentation during cold and dry periods in the Pliocene and/or Pleistocene. The strong genetic divergence between populations in southeast DR Congo could be the result of an ongoing speciation linked to ecological niche differentiation. [ABSTRACT FROM AUTHOR]

The Indo-Pacific genus Halgerda Bergh, 1880a Verhandlungen Der Koniglich-Kaiserlichen Zoologisch-Botanischen Gesellschaft in Wien 30:155–200, is one of the most diverse and better-studied genera within the nudibranch family Discodorididae. Previous studies have been predominantly based on morphology; however, the addition of molecular data has led to new species descriptions as well as unresolved species complexes. Here, we broaden the available molecular data within Halgerda by utilizing two mitochondrial and two nuclear genes in coordination with morphology to describe 14 new Halgerda species. Bayesian inference, maximum likelihood, and species delimitation analyses were used to clarify previously established relationships and evaluate the new species positions within Halgerda. Based on our results Halgerda elegans Bergh, 1905 is synonymized with Halgerda willeyi Eliot, 1904 and new descriptions for Halgerda mango sp. nov., Halgerda berberiani sp. nov., Halgerda biqiea sp. nov., Halgerda paulayi sp. nov., Halgerda labyrinthus sp. nov., Halgerda anosy sp. nov., Halgerda mesophotica sp. nov., Halgerda profunda sp. nov., Halgerda takipsilim sp. nov., Halgerda scripta sp. nov., Halgerda hervei sp. nov., Halgerda maaikeae sp. nov., Halgerda pattiae sp. nov., and Halgerda radamaensis sp. nov. are provided here. We also provide an updated morphological description for juvenile specimens of Halgerda dalanghita Fahey & Gosliner, 1999a; expand upon the two unresolved species complexes previously identified in Tibiriçá et al. (2018); and identify a new mesophotic clade in the Central Pacific. [ABSTRACT FROM AUTHOR]

The systematics of the Old World Spiranthes sinensis (Pers.) Ames species complex (Orchidaceae) has been complicated by its wide distribution and morphological variations. Within the species complex, S. australis Lindl. has been generally accepted as the only Spiranthes Rich. species distributed on the Japanese mainland. The present study provides morphological, phylogenetic, and ecological evidence for the recognition of S. hachijoensis Suetsugu as a new species of the S. sinensis species complex on the Japanese mainland. Spiranthes hachijoensis is morphologically similar to S. hongkongensis S.Y. Hu & Barretto and S. nivea T.P. Lin & W.M. Lin, sharing a degenerated rostellum, pollinia without a viscidium, and distinctly trilobed stigma. However, the taxon can be morphologically distinguished from S. hongkongensis by its glabrous rachis, ovaries, and sepals, and from S. nivea by its papillate labellum disc, larger papillate basal labellum callosities, and glabrous rachis, ovaries, and sepals. The autogamy and flowering phenology (i.e., earlier flowering) of S. hachijoensis are most likely responsible for premating isolation from the sympatric S. australis. A MIG-seq-based high-throughput molecular analysis indicated that the genetic difference between S. hachijoensis and its putative sister species S. sinensis is comparable to, or even greater than, the genetic difference between pairs of other species within the S. sinensis species complex. Our multifaceted approach strongly supports the recognition of S. hachijoensis as a morphologically, phenologically, phylogenetically, and ecologically distinct species. [ABSTRACT FROM AUTHOR]

Lampreys are an ancient lineage of jawless fish for which the relationships among some lineages are uncertain. We addressed these information gaps for Lampetra species with a focus on western North America. Phylogenetic analysis using all publicly available sequences of two mitochondrial genes—cyt b and COI—supported designation of western North American Lampetra as a distinct genus from Lampetra in Europe, Asia, and eastern North America. Species delimitation analysis of cyt b sequences identified seven species, only three of which are currently recognized. Lampetra ayresii and L. richardsoni, regarded as separate under the "paired species concept," were not genetically distinct; we recommend synonymizing L. richardsoni with L. ayresii because the latter has precedence, yet continuing to recognize each ecotype using its current common name. Other than the widespread L. ayresii clade, all other species exhibited limited ranges often restricted to one or two locations. Within headwaters of the Willamette River, L. ayresii demonstrated strong genetic structure and lack of gene flow among subbasins, indicating that the subbasin scale may represent an appropriate management unit. However, the appropriate management scale in other areas may differ based on evolutionary histories and gene flow. Subsequent work is needed across western North America to better delineate the ranges of the aforementioned species and to evaluate whether other unrecognized taxa in this lineage may be present. [ABSTRACT FROM AUTHOR]

The correct identification of species diversity of small single-celled green coccoid microalgae still causes difficulties, since their relatively simple morphology hides a high physiological, ecological and genetic diversity. The use of molecular genetic methods has revolutionized the study of the true biodiversity of so-called "small green balls," allowing the discovery of numerous new taxa. This article presents the results of a study of strains recently isolated from small freshwater urbanized lakes (Vasilievsky Lakes system, Samara region, Russian Federation). Morphologically, these strains were close to the genus Meyerella: spherical cells, cup-shaped, or wide girdle-shaped parietal chloroplast without pyrenoid. Analysis of the 18S–ITS1–5.8S–ITS2 sequences also showed that the studied strains belong to this genus. Comparison of morphological characteristics, habitat and lifestyle, analysis of tree topology, genetic distances and secondary structures of the ITS1 and ITS2 spacers of the Meyerella members, as well as the delimitation results using the Automatic Barcode Gap Discovery (ABGD) method, the Poisson Tree Processes (PTP) model, the Generalized Mixed Yule The Coalescent (GMYC) method allowed us to establish that the studied strains ACSSI 346, ACSSI 362 and ACSSI 363 are representatives of a new species – M. similis sp. nov. [ABSTRACT FROM AUTHOR]

Species are the fundamental category and the key to formulate conservation efforts. DNA and ecological niche modeling have become valuable tools for species delimitation. Wolf spiders include few web-living species, such as Aglaoctenus lagotis (Holmberg, 1876), a priority species for conservation in Uruguay. Behavioral and body coloration patterns of this species have allowed us to distinguish two groups (forms I and II). Here, we combine information from gene trees and multispecies coalescent analyses on mitochondrial (cox1, 12S, 16S + L1 + nad1) and nuclear (intron tif5A) DNA sequences, as well as from ecological niches comparisons, in order to clarify their taxonomic identity. We worked with localities in Uruguay and Argentina, including sympatric and allopatric areas. Gene trees were inferred with Maximum Likelihood, Bayesian, and statistical parsimony analyses. Molecular species delimitation analyses were conducted, and the species tree and divergence times were co-estimated. Characterization and comparison of the climatic requirements of both forms throughout annual and sexual periods were analyzed. Species delimitation and species tree analyses recovered three main lineages (Form I, Form IIa, and Form IIb). Form I is restricted to Uruguay and is closely related and sympatric with Form IIa. Form IIb is located in Argentina and in the Uruguayan west coast, generating a sympatric area of the three forms. Regarding to the sexual climatic niche, the three main lineages differ and do not overlap. Our results support the existence of more than one lineage within what is nowadays Aglaoctenus lagotis. Possible evolving processes explaining this scenario and the conservation consequences are discussed. [ABSTRACT FROM AUTHOR]

Despite the high diversity and endemism in the Mobile River Basin, analyses of molecular phylogeographic patterns of freshwater fishes in this system are lacking. Using cytochrome b (cyt b) and S7 ribosomal intron-1, this study compares the phylogeography and population structure of Etheostoma rupestre Rock Darter with a disjunct distribution throughout the Mobile River Basin. For cyt b, parsimony, Bayesian, and Species Delimitation analyses showed a split between the Tombigbee, Alabama, and Coosa/Tallapoosa Rivers, potentially representing previously undescribed species. In addition, there is evidence of limited gene flow between the lower Tombigbee/Sipsey River populations and other populations. Hierarchical comparison showed that there is genetic divergence between the major rivers of the Mobile River Basin. The lack of structure within the tributaries of the river system may indicate that Rock Darter is capable of further dispersal than typical for a darter species. The structure identified across the basin may be due to historic sea-level fluctuations and/or contemporary structure, but fine-scale, within-river analyses would be necessary to further unravel the phylogenetic relationships of the Rock Darter species complex. This study is relevant to establishing conservation guidelines for the biodiversity in the Mobile River Basin. [ABSTRACT FROM AUTHOR]

Members of Aquilaria Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. Aquilaria is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of Aquilaria is lacking. Here, we described our search for a suitable specific DNA barcode for Aquilaria species using eight complete plastome sequences. We identified five highly variable regions (HVR) (matK-rps16, ndhF-rpl32, psbJ-petA, trnD, and trnT-trnL) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, psbJ-petA and trnT-trnL, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, psbJ-petA + trnT-trnL, effectively resolved members of the genus Aquilaria by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations. [ABSTRACT FROM AUTHOR]

Background: The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories. Objective: This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool. Methods: A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species. Results: The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set. Conclusion: The COI gene should thus be used as the main barcoding marker for fighting fish. [ABSTRACT FROM AUTHOR]

Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity. [ABSTRACT FROM AUTHOR]

The genus Noctilio includes the piscivorous N. leporinus and the insectivoros N. albiventris, which have a distribution restricted to low and humid coastal areas and the main river basins in America. Considering the geographic morphometric variation and the molecular divergence previously documented in genus Noctilio, we analyze two-dimensional geometric configurations of cranial characters to assess if the amount of morphological variation or the existence of morphological discontinuities within Noctilio species is compatible with the possible existence of several species, as well as their relationships in a combined phylogenetic reconstruction. The shape and size variation of cranial characters supports differences among two of three molecular lineages previously reported in N. albiventris—one distributed in Central America and North of South America, and the other distributed in South America. We also recover differences between the two mitochondrial clades for N. leporinus, one distributed from Mexico to the west side of the Andes and the Greater Antilles, and the other to the eastern side of the Andes and the Lesser Antilles. Based on the combined phylogeny, we recover the paraphyly of N. albiventris, composed of two morphologically differentiated taxa, and the monophyly of N. leporinus, composed of two morphologically divergent lineages. The latitudinal position and environmental variables correlate with cranial variation and support the geographic pattern of differentiation in the evolutionary history of Noctilio. [ABSTRACT FROM AUTHOR]

Hydnum repando-orientale is an East Asian species closely related to H. boreorepandum and H. repandum; all three species produce edible mushrooms. We identified two ecological groups of H. repando-orientale in Japan: a temperate group occurring in Fagaceae-dominated forest at < 1200 m a.s.l. (ROF) and a subalpine group occurring in coniferous forest in highland at > 1900 m a.s.l. (ROC). We re-examined the taxonomy of the two ecological groups of H. repando-orientale using integrative approaches. Phylogenies of the two ecological groups and other related species were inferred from the internal transcribed spacer (ITS) and gene portions encoding the large subunit of nc rRNA (LSU), translation elongation factor-1 alpha (TEF1), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second-largest subunit (RPB2). The concatenated phylogenetic tree separated the two ecological groups into well-supported sister clades. Also, species delimitations based on the topological congruence (GCPSR) and coalescent models (GMYC and BP&P) supported to separate the two ecological groups. Morphological analysis showed that ROC specimens had significantly larger basidiospores, compared with ROF specimens. Mon-mon mating tests using six ROF, three ROC, and three H. boreorepandum strains each showed independent incompatible groups, whereas one ROC strain showed compatibility with both ROC and ROF populations. Based on these results, we defined the ROC group as a new species, H. subalpinum. Because H. repando-orientale and H. subalpinum have smaller genetic divergence in nc rDNA and maintain slight sexual compatibility, they may have recently speciated in East Asia. [ABSTRACT FROM AUTHOR]

Wetlands are present in different parts of the globe, holding a significant portion of the local biodiversity, and have been under the constant influence of climatic changes worldwide on different time scales. Investigations with a phylogeographic approach have revealed the role of Quaternary climatic shifts on a global scale, favoring constant changes in the amplitude of floodplains and affecting the evolutionary history of multi-taxa. This pattern was observed in the Amazonian biota, but due to the complex geological history, some of these models alone are insufficient, especially in widespread species that live in specific regions of the biome. Herein, we investigated the species delimitation and biogeographic history of the semi-aquatic lizard Uranoscodon superciliosus (U. superciliosus), widely distributed in Amazonian floodplains, a habitat that was for a long time considered a corridor to gene flow. Our results support a high genetic diversity with five well-supported lineages within U. superciliosus: North of the Amazon River, East Xingu, Solimões, Purus, and Tapajós-Madeira, with the basal split within this group in the Miocene and others in the Plio-Pleistocene. These results corroborated a mixture of distinct processes that shaped the diversity of U. superciliosus with rivers as vicariant barriers and the already known role of paleoclimatic shifts during the Quaternary promoting diversification. Among tetrapods, our work is one of the first to describe the genetic structure in a widespread taxon along river-edge environments, thus supporting both patterns of diversification with the compartmentalized lineages along different Amazonian rivers (floodplains) and also the more common pattern found in upland forest species, with main rivers acting as vicariant barriers and playing a role in allopatric speciation. [ABSTRACT FROM AUTHOR]

The deep-sea holothurian Chiridota heheva Pawson & Vance, 2004 was recently recognised as a cosmopolitan species which exploits the organic enrichment at three types of deep-sea reducing environments: hydrothermal vents, cold seeps, and organic falls. Here, we apply phylogenetic reconstruction and species delimitation approaches using new COI and 12S sequence data to show that C. heheva is genetically congruent with the only other hydrothermal vent holothurian, Chiridota hydrothermica Smirnov & Gebruk, 2000, with strong supporting morphological, ecological, and biogeographical parallels between the two. As such, we propose that C. heheva is a junior synonym of C. hydrothermica, and that subsequent chiridotid holothurians discovered at deep-sea reducing environments likely also belong to this single globally distributed species. As a species endemic to deep-sea reducing environments yet known at sites across the Atlantic, Indian, and Pacific Oceans, this unique holothurian provides an interesting case study for connectivity, biogeography, and speciation in the deep sea, which has important implications for deep-sea conservation planning. [ABSTRACT FROM AUTHOR]

The evolutionary relationships of the nudibranch genus Dondice Er. Marcus, 1958, its hypothesized synonym with Nanuca Er. Marcus, 1957, as well as its species-level diversity remain unresolved. Here, in order to assess the systematics of Dondice a molecular phylogenetic analysis based on cytochrome c oxidase I and 16S genes was carried out, including various representatives of the Myrrhinidae. As a result, Dondice is monophyletic and a valid genus, presenting morphological diagnostic features when compared to Nanuca. An integrative taxonomic approach focused on Western Atlantic Dondice occidentalis (Engel, 1925) and Dondice parguerensis Brandon & Cutress, 1985, including a broader geographic and morphological range of specimens, indicates that D. occidentalis constitutes a complex of six pseudocryptic species with geographically restricted ranges across the Western Atlantic, and D. parguerensis is a distinct, valid species. Dondice occidentalis s. str. is recognized as the species of the genus with the largest morphological variation, whereas the five new species, Dondice arianeae sp. nov., Dondice freddiemercuryi sp. nov., Dondice juansanchezi sp. nov., Dondice jupiteriensis sp. nov., and Dondice caboensis sp. nov. exhibit consistent morphological patterns, in agreement with molecular distinctiveness. Our study increases the number of known species of Dondice from four to nine and highlights the importance of addressing marine biodiversity within an integrative framework. [ABSTRACT FROM AUTHOR]

The Ethiopian highlands represent the largest part of the Eastern Afromontane Biodiversity Hotspot (EAMBH). Their fauna and flora are largely unique. Particularly, Afroalpine habitats on isolated mountains are known to harbour a large number of highly specialized endemic species. In contrast to intensively studied Afroalpine ecosystems, the forests in southern and southwestern parts of the Ethiopian highlands remain neglected in terms of biodiversity research, even though they represent the only remaining natural large-scale forests in this part of EAMBH. Here, we performed an integrative taxonomic revision (combining multi-locus phylogenetic analysis with classical and geometric morphometrics) and analysis of the evolutionary history of ancient lineages of the genus Mus, with a special focus on the taxon discovered in moist Ethiopian forests. We unequivocally showed that this taxon forms a very distinct gene pool separated from other taxa by the mid-Pliocene, substantially differentiated from both sympatric and sister species by external and cranial morphology. None of the available type specimens (including synonym types) can be unambiguously classified to this taxon according to both skull and body form. Therefore, we describe it as a new mammal species, narrowly endemic to two most humid forests in southern (Harenna) and southwestern (Chingawa) part of the Ethiopian highlands. The description of such paleo-endemic taxa will add incentives to embark on urgent conservation action for formal protection of these unique forests within the EAMBH. [ABSTRACT FROM AUTHOR]

Octocorals are conspicuous members of coral reefs and deep-sea ecosystems. Yet, species boundaries and taxonomic relationships within this group remain poorly understood, hindering our understanding of this essential component of the marine fauna. We used a multifaceted approach to revisit the systematics of the Caribbean octocorals Plexaura homomalla and Plexaura kükenthali, two taxa that have a long history of taxonomic revisions. We integrated morphological and reproductive analyses with high-throughput sequencing technology to clarify the relationship between these common gorgonians. Although size and shape of the sclerites are significantly different, there is overlap in the distributions making identification based on sclerites alone difficult. Differences in reproductive timing and mode of larval development were detected, suggesting possible mechanisms of pre-zygotic isolation. Furthermore, there are substantial genetic differences and clear separation of the two species in nuclear introns and single-nucleotide polymorphisms obtained from de novo assembled transcriptomes. Despite these differences, analyses with SNPs suggest that hybridization is still possible between the two groups. The two nascent species also differed in their symbiont communities (genus Breviolum) across multiple sampling sites in the Caribbean. Despite a complicated history of taxonomic revisions, our results support the differentiation of P. homomalla and P. kükenthali, emphasizing that integrative approaches are essential for Anthozoan systematics. [ABSTRACT FROM AUTHOR]

Scleractinian corals provide habitats for a broad variety of cryptofauna, which in turn may contribute to the overall functioning of coral symbiomes. Among these invertebrates, hydrozoans belonging to the genus Zanclea represent an increasingly known and ecologically important group of coral symbionts. In this study, we analysed 321 Zanclea colonies associated with 31 coral genera collected from 11 localities across the Indo-Pacific and Caribbean regions, and used a multi-disciplinary approach to shed light on the evolution and biogeography of the group. Overall, we found high genetic diversity of hydrozoans that spans nine clades corresponding to cryptic or pseudo-cryptic species. All but two clades are associated with one or two coral genera belonging to the Complex clade, whereas the remaining ones are generalists associated with both Complex and Robust corals. Despite the observed specificity patterns, no congruence between Zanclea and coral phylogenies was observed, suggesting a lack of coevolutionary events. Most Zanclea clades have a wide distribution across the Indo-Pacific, including a generalist group extending also into the Caribbean, while two host-specific clades are possibly found exclusively in the Red Sea, confirming the importance of this peripheral region as an endemicity hotspot. Ancestral state reconstruction suggests that the most recent common ancestor of all extant coral-associated Zanclea was a specialist species with a perisarc, occurring in what is now known as the Indo-Pacific. Ultimately, a mixture of geography- and host-related diversification processes is likely responsible for the observed enigmatic phylogenetic structure of coral-associated Zanclea. [ABSTRACT FROM AUTHOR]

Dorcadionini is a highly speciose tribe within Cerambycidae and is also one of the most challenging in terms of species identification owing to the large number of taxa, intraspecific variability or similarity between species. To support species identification and taxonomic decisions, we generated DNA barcodes for 24 species and 152 specimens. Cases of disagreement between the barcode and taxonomic species were further analysed with the 28S and internal transcribed spacer 2 (ITS2) nuclear markers. The mitochondrial variation is mostly in accordance with the traditional taxonomy except a case of haplotype sharing between Dorcadion murrayi, Dorcadion axillare and Dorcadion pusillum that suggest hybridisation events. We hypothesise that introgression is the likely explanation for part of the large morphological variability found in many other species. In Dorcadion aethiops and Dorcadion fulvum, the taxonomic subspecies are not distinguishable using molecular data, as the haplotypes are identical or very similar, while in Dorcadion equestre, the subspecific structure is in accordance with the genetic data. A low between-species divergence ranging from 0.62 to 2.38% was found in four species, in contrast with the deep intraspecific divergences in D. equestre. We use two methods for single-locus species delimitation (General Mixed Yule Coalescent and Poisson Tree Processes), but none was perfect as both have shortcomings in oversplitting or lumping species. Dorcadion fulvum fulvum is confirmed for Romania. [ABSTRACT FROM AUTHOR]

Nothapodytes (Icacinaceae) is a genus of seven to eleven evergreen or deciduous tree species distributed in tropical Asia from India to Japan. Nothapodytes nimmoniana sensu lato is the most widespread species of the genus, being reported sporadically throughout South Asia, Southeast Asia, Taiwan, and Japan’s southwest islands. Nothapodytes amamianus was recently described from Amami-oshima, Japan, the northeastern edge of this widespread species’ range. However, the phylogenetic distinction between these two species has yet to be explored. Here we present an analysis of molecular species delimitation to test the morphology-based taxonomic hypothesis currently used to differentiate the two species. The results clearly show that N. nimmoniana sensu lato comprises two species, one in India and the other in Taiwan and Japan, including N. amamianus, requiring a reassessment of the morphological traits hitherto used to define the former and distinguish it from the latter in East Asia. Based on the taxonomic history of the taxa and rules of nomenclature, the name N. nimmoniana is retained for the former. We propose a new combination, N. insularis, for the latter. Longitudinal intraspecific geographic structure is highlighted as an apparent indicator of further hidden diversity in India’s Western Ghats. [ABSTRACT FROM AUTHOR]

Given the difficulties for rapid biodiversity assessments in understudied regions, DNA barcoding appears as a suitable alternative. Still, this approach relies heavily on accurate reference sequence databases for correct taxonomic assignments. In this study, we evaluated the effectiveness of matK, rbcL, and ITS regions for the identification of Myrtaceae species with emphasis on the megadiverse genus Syzygium from Sumatra, Indonesia; and analyzed the applicability of species-tree inference for species assignment using barcode markers. ITS was the most variable barcode region (42.6% of variable sites), followed by matK (25.7%), and rbcL (14.9%). In terms of assignments of sequences using the BLAST algorithm, all markers were effective for genus-level attribution. For assignments at species rank, rbcL was able to attribute 30.15% of the samples at the species level, followed by matK (26.47%), and ITS (17.21%). These results are largely related to the availability of reference sequences for Myrtaceae in the databases since for the 27 species analyzed in this study, only 8 species had reference sequences for all three barcode regions available in GenBank. The species-tree inference based on the combination of matK, rbcL, and ITS markers recovered 41% of the species as monophyletic clades with strong node support. Due to its high level of differentiation, we recommend the ITS region as the most efficient barcode marker for the identification of Syzygium, and the traditional core-barcodes (matK + rbcL) as add-on barcodes. [ABSTRACT FROM AUTHOR]

The genus Morchella has gone through turbulent taxonomic treatments. Although significant progress in Morchella systematics has been achieved in the past decade, several problems remain unresolved and taxonomy in the genus is still in flux. In late 2019, a paper published in the open-access journal Scientific Reports raised serious concerns about the taxonomic stability of the genus, but also about the future of academic publishing. The paper, entitled "High diversity of Morchella and a novel lineage of the esculenta clade from the north Qinling Mountains revealed by GCPSR-based study" by Phanpadith and colleagues, suffered from gross methodological errors, included false results and artifactual phylogenies, had misapplied citations throughout, and proposed a new species name invalidly. Although the paper was eventually retracted by Scientific Reports in 2021, the fact that such an overtly flawed and scientifically unsound paper was published in a high-ranked Q1 journal raises alarming questions about quality controls and safekeeping procedures in scholarly publishing. Using this paper as a case study, we provide a critical review on the pitfalls of Morchella systematics followed by a series of recommendations for the delimitation of species, description of taxa, and ultimately for a sustainable taxonomy in Morchella. Problems and loopholes in the academic publishing system are also identified and discussed, and additional quality controls in the pre- and post-publication stages are proposed. [ABSTRACT FROM AUTHOR]

Scientific names are crucial for communicating knowledge concerning fungi and fungus-like organisms. In plant pathology, they link information regarding biology, host range, distribution and potential risk to agriculture and food security. In the past, delimitation among pathogenic taxa was primarily based on morphological characteristics. Due to distinct species sharing overlapping characteristics, the morphological identification of species is often neither straightforward nor reliable. Hence, the phylogenetic species concept based on molecular phylogenetic reconstructions gained importance. The present opinion discusses what a fungal species is and how identification of species in plant pathology has changed over the past decades. In this context, host-specialization and species complexes are discussed. Furthermore, species concepts in plant pathology are examined using case studies from Bipolaris, Colletotrichum, Curvularia, Diaporthe, Diplodia, Meliola, Plasmopara, rust fungi and Trichoderma. Each entry contains a brief introduction to the genus, concepts used in species identification so far and the problems in describing a species followed by recommendations. The importance of correctly naming and identifying a species is addressed in the context of recent introductions, and we also discuss whether the introduction of new species in pathogenic genera has been overestimated. We also provide guidelines to be considered when introducing a new species in a plant pathogenic genus. [ABSTRACT FROM AUTHOR]

Alhagi Gagnebin (Fabaceae: Hedysareae) is a small genus of shrubs or subshrubs distributed in temperate and tropical regions of Asia, Europe, and Africa. The exact number of Alhagi species in Iran has been disputable. Studies showed that morphology, seed protein, and chromosome characters could not clearly delimitate the species boundaries of the genus. In order to determine species boundaries and the population structure of Alhagi species in Iran, eight labeled inter simple sequence repeat (ISSR) primers were used to screen 22 populations including 110 individuals. STRUCTURE, PCoA and clustering analyses of ISSR data were able to clearly split all populations of Alhagi in Iran into two distinct groups. As the populations A. pseudalhagi and A. maurorum jointly formed a group (A. maurorum complex) segregated from those of Alhagi graecorum. Further analyses of A. maurorum complex showed a significant molecular difference among the studied populations (PhiPT value = 0.213, P = 0.001) as well as a high amount of variability within populations (79%) indicating frequent genetic exchanges. Structure analysis of complex populations (K = 2) showed no distinct genetic pattern related to their geographical distribution. In this study, Alhagi has retrieved the only two species of Alhagi in Iran; A. graecorum and A. maurorum. [ABSTRACT FROM AUTHOR]

Hymenocrater comprises of 11 species throught the world. The genus is an Irano-Turanian elements, which has several usages in traditional medicine. Northeast of Iran is the main geographical region of Hymenocrater species. The aims of the peresent study was to delimit 11 species of Hymenocrater to determine the species relationships based on morphological and molecular data (cp-DNA sequence), to produce divergence time and to construct barcode gap using the internal transcribed sequence because of adulteration of this genus in local markets. According to the results, Neighbor-Net network and UPGMA dendrogram of morphological data can delimit Hymenocrater species. Meanwhile, analyses of Chloroplast sequences (psbA-trnH) revealed that the species relationship and delimitation are difficult and complicated due to gene flow, hybridization, gene duplication, reticulation and chloroplast capture. Divergence time of Hymenocrater species estimated from Bayesian Evolutionary Sampling Trees date were seven million years ago. The center origin of Hymenocrater in Iran is Razavi Khorasan. Genetic fingerprinting of correctly identified medicinal species provides standard for comparing plant specimens sold in the market with true to type medicinal plant. Therefore, ITS sequences are important for barcoding this medicinally significant plant. It is correctly identified medicinal species, which will be used as standard for evaluating market sold plants. [ABSTRACT FROM AUTHOR]

Available ecological information, an extensive distributional range, conflicting osteological data, and a proposed early Miocene origin provide the impetus for the present study which investigates genetic structuring, biogeographic, and phylogenetic relationships within the Aplocheilichthys spilauchen lineage. Through the analysis of the mitochondrial gene COI, species delimitation methods (ABGD, GB, GMYC, bPTP) were applied, recognizing 6–7 OTUs with absolute pairwise genetic distances ranging between 8 and 22%. The onset of diversification is estimated to be within the middle Miocene and both dispersal and vicariance-shaped A. spilauchen diversity and distribution, as suggested by time-calibrated and ancestral range reconstruction (S-DIVA) analyses. We report for the first time, a pattern of diversification within a lineage of brackish water fish that is concordant with the historical distribution of coastal mangroves forests, shaped by a series of historical events that likely affected forest cover since the middle Miocene (e.g. major climate shifts and sea-level fluctuations, onset of the modern Congo River outlet, increased volcanism in the Cameroon Volcanic Line). [ABSTRACT FROM AUTHOR]