Phylogenomics-guided revision of the genus Rhytisma Alderslade, 2000 (Octocorallia: Malacalcyonacea: Lemnaliidae), with descriptions of six new species.

Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences from Hainan Island in the South China Sea and previously published ones from Japan, Taiwan, Singapore, the Philippines, Indonesia, Australia, the Solomon Islands and the Red Sea. Three nominal species, Tridacna crocea, T. squamosa and T. noae, were recognized at Hainan Island on the basis of distance-based DNA barcoding, with mean interspecific K2P distances of 10.6–24.7% for seven Tridacna species (T. crocea, T. squamosa, T. noae, T. maxima, T. mbalavuana, T. derasa and T. gigas). The most abundant species, T. noae, represents the first record of this species from Hainan Island. Using a combination of phylogenetic and DNA-based species delimitation analyses (automatic barcode gap discovery, generalized mixed Yule coalescent and Bayesian Poisson tree processes), we found strong support for a total of 13 operational taxonomic units (OTUs) for the seven nominal Tridacna species. These results, coupled with the fact that each OTU occupies different regions in the Indo-Pacific, strongly suggest multiple cryptic species of giant clams. Our findings point to the need for taxonomic revisionary work on giant clams throughout the Indo-Pacific; such work will have important conservation implications.

Trombiculid mites (Acariformes) are unique among arthropods of medical importance in that only the larval instar (chigger) is parasitic, which can result in the transmission of zoonotic scrub typhus. The use of molecular approaches for chigger species discrimination has been very limited until recently, especially for those parasitizing bird hosts, where data remain scarce. Here, we aimed to generate DNA barcodes of chiggers parasitizing birds in Malaysia based on the mitochondrial cytochrome c oxidase subunit I (COI) gene following DNA extraction, PCR and sequencing. Fifty-four COI sequences from 8 bird-associated chigger species in Malaysia were combined with 50 GenBank sequences comprising 7 genera from various countries for DNA barcode and phylogenetic analysis. The correct identification rates for the 95 COI barcodes were 96.84% (Best Match) and 86.31% (Best-Close Match). DNA barcode analyses effectively clustered the 8 nominal species from this study into their respective genera. Genetic divergence of less than 3% was observed within Ascoschoengastia lorius, Neoschoengastia gallinarum, Parascoschoengastia heynemani, Leptotrombidium imphalum, and Blankaartia acuscutellaris, all of which formed a monophyletic clade, confirming their conspecific nature. Conversely, intraspecific divergences of 17.64%, 15.49%, and 11.63% were obtained for Toritrombicula densipiliata, Odontacarus audyi, and Leptotrombidium deliense. These divergences, supported by evidence of distinct entities through delimitation analyses, indicate potential cryptic diversity within these populations. In conclusion, this study represents the first molecular genetic analysis of bird chiggers in Malaysia, revealing varying levels of genetic divergence. Our findings highlight the utility of DNA barcoding for understanding chigger diversity and aiding in accurate identification.

Objective Protecting biodiversity is important for preserving ecosystem functions and services, and understanding the diversity present in a system is necessary for effective conservation. Lampreys display extensive diversity in morphology and life history strategy. The extent of this diversity and the underlying genetic patterns have not yet been fully characterized. Uncertainty about species boundaries and operational taxonomic units hinders lamprey management and conservation. Limited data have been collected on California lampreys (Lampetra spp. and Entosphenus spp.), but evidence suggests widespread population decline across the west coast of North America. Study objectives were to identify which nominal species are present at study sites across northern and central California, determine whether current taxonomic classifications accurately and sufficiently describe lamprey diversity in California, and characterize the biogeographic distribution of genetically distinct lamprey lineages across the study area. Methods To achieve these objectives, this study utilized DNA barcoding, phylogenetic analysis, and species delimitation analysis. Lamprey individuals (N = 87) from 19 sites in the Sacramento–San Joaquin River basin, San Francisco Bay, and Klamath River basin were sequenced for the mitochondrial cytochrome b (cyt b) gene, and the data were combined with publicly available lamprey cyt b sequences for analysis. Result Results showed relatively deep phylogenetic divergence between Lampetra and Entosphenus. Distinct and genetically divergent lineages were observed within Lampetra, while distinct but genetically similar lineages were observed within Entosphenus. This study revealed novel Lampetra lineages in the Napa River and Alameda Creek, and results suggest that the biogeographic distribution of lamprey diversity may follow patterns observed in other native fishes. Species delimitation results indicated that at least seven separate candidate species of Lampetra can be found in California, suggesting that California holds more species-level diversity than the expected three nominal Lampetra species known to occur in the state. Conclusion These results highlight the underestimated diversity of lampreys in California and the need for further assessment of taxonomic classifications and operational taxonomic unit designations of California lampreys.

The Madrean Sky Islands of northern Mexico and the south‐western United States are located in the Madrean pine–oak woodlands ‘biodiversity hotspot’. This area is renowned for its exceptional flora and fauna, but comparatively little is known about arthropod diversity in this region. We obtained specimens of the tarantula genus Aphonopelma from five different mountain ranges (Huachucas, Pajaritos, Peloncillos, Santa Catalinas, and Santa Ritas) to assess patterns of diversity within the group. Species delimitation in tarantulas is difficult because they possess few informative morphological features. We implemented a rigorous methodological framework for delimiting species that incorporated multiple lines of evidence (molecules, distributional information, morphology, and breeding period) in an explicitly hypothesis‐driven manner. Our integrative taxonomic approach delimited three species (all undescribed): one endemic to the Peloncillos, one endemic to the Santa Catalinas, and one that is more widely distributed in the Huachucas, Santa Ritas, and Pajaritos. These patterns of diversity and endemicity are comparable to other arachnids in the region and suggest that species‐level diversity of stenotypic/dispersal‐limited arthropods throughout the Madrean Sky Island Region may be underestimated. Ecological data are not widely available for Madrean Sky Island tarantulas and it is difficult to evaluate their conservation status. Several intrinsic (patterns of endemicity, limited vagility, and life history) and extrinsic (habitat degradation, commercial exploitation, and climate change) factors, however, suggest that these spiders may be of conservation concern. The approach taken in this study highlights the importance of considering multiple lines of evidence when species delimitation has direct implications on conservation.

Species delimitation in the Eviota sigillata species complex, a widely distributed group of cryptobenthic coral reef fishes.

The genus Apharyngostrigea comprises a group of diplostomoidean digeneans that parasitize birds of the family Ardeidae (herons), with approximately 20 species described worldwide. Despite numerous efforts, a robust phylogenetic framework to delimit species within the genus is still lacking, mainly due to the limited morphological variation among its members. This study employed an integrative taxonomic approach, combining nuclear and mitochondrial DNA sequences with morphological data to assess species boundaries within Apharyngostrigea based on specimens collected from southeastern Mexico. Using a combination of species discovery (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partition, General Mixed Yule Coalescent and Poisson Tree Processes) and validation methods based on Bayesian gene tree topologies (BPP and PHRAPL). We found high diversity within this genus in southeastern Mexico. Our analyses supported the delimitation of four nominal species that were previously described and validated in this study, along with the redescription of three of them. In addition, through species delimitation methods and morphological examination, we identified two candidate species and/or lineages that require further evidence to be formally described. This study demonstrates that an integrative taxonomic approach provides a robust framework for species delimitation in taxonomically complex groups such as Apharyngostrigea.

Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment - parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.

In order to well identify the 93 wild Cortex Daphnes samples from different species and habitats in western China and develop a standard operating procedure (SOP) for the authentication and quality of them in the future, a comprehensive and efficient identification system based on DNA barcoding and HPLC fingerprint technologies has been developed. The result showed that only 17 samples (18%) were Daphne giraldii Nitsche (DG), which is recorded in Chinese Pharmacopeia, while the others (82%) might have safety hazards. Additionally, the result of HPLC fingerprint analysis indicated that samples in the same species origins and wild distributions could be clustered together, which was consistent with DNA barcoding analysis. The study can provide a significant system for the authentication and quality of commercial Cortex Daphnes herbs. Undoubtedly, this study undoubtedly confirmed that the chemical compositions of Cortex Daphnes herbs were affected by both species origins and ecological environments, which is required more in-depth research.

The increasing world market demand for seafood requires an expansion of product categories available to consumers. Inland fish are usually considered having unmarked taste and are less appreciated by consumers; thus, they have low commercial value. Therefore, the marketing of the lake’s fresh and processed fish is limited to the local market and consumers are currently uninformed and mistrustful about these species. In this study, six different fish species were caught in the Fondi lake (Lazio, central Italy): Anguilla anguilla, Tinca tinca, Carassius gibelio, Cyprinus carpio, Micropterus salmoides, Chelon ramada. All the samples were subjected to nutritional and DNA barcoding analysis. Moisture, protein, fat, carbohydrates, ash, and sodium content were measured. As regards the fatty acids profile, the most abundant were MUFAs with the highest value in Anguilla anguilla (45.97%). Oleic acid (C18: 1 n9 cis) was particularly high in Cyprinus carpio (55.46%). The fraction of polyunsaturated fatty acids (PUFA) revealed a higher DHA content (C22: 6 n3) in Anguilla anguilla than the other species (>12 %) while Chelon ramada presented both higher EPA content (C 20: 5 n3) and total fraction of omega 3 PUFAs. Concerning molecular analysis, a 655 bp fragment of cytochrome C oxidase subunit I (COI) gene was successfully used for the identification at the species level using both BOLD and BLAST public databases. The present study gives the basis for improving the knowledge and promoting inland fish’ market and traceability along the supply chain.

Simple SummaryThe catfish of the genus Pimelodus are amply distributed in the Neotropical region, although the species-level taxonomy and phylogenetic relationships of these fish are still poorly resolved. In the present study, we used a molecular approach to delimit the Pimelodus species from the different river basins of the Neotropical region. For this, we analyzed sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene from 13 nominal species, which generated 24 consensus Molecular Operational Taxonomic Units (MOTUs). Only six of the nominal species were recovered as well-defined molecular entities, while seven presented cryptic diversity or taxonomic uncertainties. The DNA barcode analysis presented here represents an important step toward the definition of the species of this economically important group of fish, which will be fundamental to the conservation of its diversity.Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.

The Wet Tropics bioregion of north‐eastern Australia has been subject to extensive fluctuations in climate throughout the late Pliocene and Pleistocene. Cycles of rainforest contraction and expansion of dry sclerophyll forest associated with such climatic fluctuations are postulated to have played a major role in driving geographical endemism in terrestrial rainforest taxa. Consequences for the distributions of aquatic organisms, however, are poorly understood. The Australian non‐biting midge species Echinocladius martini Cranston (Diptera: Chironomidae), although restricted to cool, well‐forested freshwater streams, has been considered to be able to disperse among populations located in isolated rainforest pockets during periods of sclerophyllous forest expansion, potentially limiting the effect of climatic fluctuations on patterns of endemism. In this study, mitochondrial COI and 16S data were analysed for E. martini collected from eight sites spanning the Wet Tropics bioregion to assess the scale and extent of phylogeographic structure. Analyses of genetic structure showed several highly divergent cryptic lineages with restricted geographical distributions. Within one of the identified lineages, strong genetic structure implied that dispersal among proximate (<1 km apart) streams was extremely restricted. The results suggest that vicariant processes, most likely due to the systemic drying of the Australian continent during the Plio‐Pleistocene, might have fragmented historical E. martini populations and, hence, promoted divergence in allopatry.

Molecular studies have improved our knowledge on the neotropical ichthyofauna. DNA barcoding has successfully been used in fish species identification and in detecting cryptic diversity. Megaleporinus (Anostomidae) is a recently described freshwater fish genus within which taxonomic uncertainties remain. Here we assessed all nominal species of this genus using a DNA barcode approach (Cytochrome Oxidase subunit I) with a broad sampling to generate a reference library, characterize new molecular lineages, and test the hypothesis that some of the nominal species represent species complexes. The analyses identified 16 (ABGD and BIN) to 18 (ABGD, GMYC, and PTP) different molecular operational taxonomic units (MOTUs) within the 10 studied nominal species, indicating cryptic biodiversity and potential candidate species. Only Megaleporinus brinco, Megaleporinus garmani, and Megaleporinus elongatus showed correspondence between nominal species and MOTUs. Within six nominal species, a subdivision in two MOTUs was found, while Megaleporinus obtusidens was divided in three MOTUs, suggesting that DNA barcode is a very useful approach to identify the molecular lineages of Megaleporinus, even in the case of recent divergence (< 0.5 Ma). Our results thus provided molecular findings that can be used along with morphological traits to better define each species, including candidate new species. This is the most complete analysis of DNA barcode in this recently described genus, and considering its economic value, a precise species identification is quite desirable and fundamental for conservation of the whole biodiversity of this fish.

Manufacturers aim to design implants fitting for the broadest possible population segment. Due to the scarcity of available morphological data of intact long bones, anatomical collections of historical bone specimens may represent valuable additional sources. Previous work on femoral morphology measurements suggests that historical specimens are widely consistent with data from present-day populations. This study aimed to investigate whether this also applies to the anatomical fitting of a clinically used femoral nail. Nail fit was computer-graphically quantified through virtual implantation into CT-based 3D models of 52 femora, comprising a subset representative of the present-day Caucasian population (n = 31), a subset from a historical medieval European bone collection (n = 20), and additionally, a dataset from a natural ice mummy from the Neolithic period. Nail fit was assessed by nail protrusion (area and distance) to the inner cortex surface and the distal nail tip's position in the medullary canal. Assessed measurements and parameters of the present-day Caucasian subset were mostly consistent with those of the medieval European subset. After adjusting for multiple testing, only the distance from lateral nail entry point to shaft axis remained significantly (p = 0.03) different when comparing our modern and medieval subsets. Subsequent bivariate (Spearman) correlation analyses for both subsets (modern and medieval) combined showed that of the three variables representing basic demographic parameters, individual age, biological sex, and femur length, most statistically significant associations to the examined nail fit measurements were found for age (six measurements at a level of p < 0.05), however, with a relatively weak monotonic correlation (rho values ranging between ±0.31 and ±0.37). The measurements for the Iceman's femur lie within the range of the modern and historical subgroups, but in some cases, differ by more than one standard deviation from the mean. Our results confirm previous findings, suggesting that more recent historical bone specimen collections may indeed be a convenient and easily accessible source of new 3D morphological data and complement existing data to be used for the development of femoral nails.

This study combines phylogenetic analyses of mitochondrial DNA sequences with comparative morphological analyses to revise the taxonomy of 101 nominal siphonariid species from the Indo-West Pacific belonging to the genera Siphonaria Sowerby I, 1823 and Williamia Monterosato, 1884. We have examined preserved specimens that have been newly collected at 462 sites across Australasia, the Indo-West Pacific, and in temperate zones of the northern and southern Pacific. Critically, our sampling includes topotypic specimens of 98 nominal species. The study area covered herein extends between the latitudes of 60°N and 55°S and the longitudes of 37°E and 175°W. We have sequenced two mitochondrial genes (COI and 16S) from 546 individuals and conducted a phylogenetic analysis including additional sequences from GenBank. We also studied the anatomy of 436 individuals using dissections and scanning electron microscopy. This study offers a comprehensive documentation and taxonomic assessment of type specimens for nearly all examined nominal species. Our taxonomic revision leads us to accept 88 species, which are thoroughly redescribed. 52 nominal species are treated as synonyms of earlier names, 41 of which are newly synonymized herein. Thirteen species names are deemed unavailable or invalid under the rules of zoological nomenclature, and six names are considered as nomina dubia or nomina inquirenda, notably including the oldest name, Patella laciniosa, which was widely used previously. In addition, we describe 40 new species. We have identified eleven species with broad distributions in the IWP and beyond and four species with more limited distributions than previously accepted. Notably, many species have narrow ranges, some being single island endemics. To stabilize taxonomic names, we have designated neotypes for seven species (Siphonaria sipho Sowerby I, 1823, Patella japonica Donovan, 1824, S. obliquata Sowerby I, 1825, Pileopsis radiata Blainville, 1826, S. radians H. Adams &amp; A. Adams, 1855, S. incerta Deshayes, 1863, and S. tasmanica Tenison Woods, 1877) and lectotypes for 25 species (Patella javanica Lamarck, 1819, S. albicante Quoy &amp; Gaimard, 1833, S. atra Quoy &amp; Gaimard, 1833, S. capensis Quoy &amp; Gaimard, 1833, S. denticulata Quoy &amp; Gaimard, 1833, S. diemenensis Quoy &amp; Gaimard, 1833, S. guamensis Quoy &amp; Gaimard, 1833, S. plana Quoy &amp; Gaimard, 1833, S. plicata Quoy &amp; Gaimard, 1833, S. punctata Quoy &amp; Gaimard, 1833, S. viridis Quoy &amp; Gaimard, 1833, S. savignyi Krauss, 1848, S. cancer Reeve, 1856, S. bifurcata Reeve, 1856, S. funiculata Reeve, 1856, S. kurracheensis Reeve, 1856, S. lirata Reeve, 1856, S. scabra Reeve, 1856, S. belcheri Hanley, 1858, S. nuttallii Hanley, 1858, S. nigerrima Smith, 1903, S. madagascariensis Odhner, 1919, S. alba Hubendick, 1943, M. lentulus Iredale, 1940, H. monticulus Iredale, 1940 and M. oppositus Iredale, 1940).

BackgroundDelimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma “humboltianum group” (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau.ResultsOur results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system.ConclusionsOverall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.