In this work, we describe a new species of the genus Oreonectes, Oreonectes yuedongensis sp. nov., collected from the Lianhua Mountains in eastern Guangdong, China. Phylogenetic trees constructed based on the mitochondrial cytochrome b (Cyt b) gene showed that this new species represents an independent evolutionary lineage, with uncorrected genetic distances (Kimura 2-parameter model) from congeners ranging from 5.1% to 8.3%. In addition, nuclear DNA analysis indicated O. yuedongensis as an independent lineage separate from its closely related species. Morphologically, the new species can be distinguished from other six species in the genus Oreonectes by a combination of serial characters. The description of this new species suggests that it is necessary to reassess the biodiversity of Oreonectes platycephalus as a complex, especially in the middle reaches of the Pearl River near the border between Guangdong and Guangxi. Morphological and genetic evidence supports O. yenlingi as a synonym of O. platycephalus.

The Chiricahua Mountains in southeastern Arizona are renowned for their exceptional biodiversity and high levels of endemism. Morphological, genomic, behavioral, and distributional data were used to report the discovery of a remarkable new tarantula species from this range. Aphonopelmajacobii sp. nov. inhabits high-elevation mixed conifer forests in these mountains, but also co-occurs and shares its breeding period with A.chiricahua-a related member of the Marxi species group-in mid-elevation Madrean evergreen oak and pine-oak woodlands. This marks the first documented case of syntopy between two montane endemics in the Madrean Archipelago and adds to our knowledge of this threatened region\'s unmatched tarantula diversity in the United States. An emended diagnosis and redescription for A.chiricahua are also provided based on several newly acquired and accurately identified specimens. Phylogenetic analyses of mitochondrial and genomic-scale data reveal that A.jacobii sp. nov. is more closely related to A.marxi, a species primarily distributed on the Colorado Plateau, than to A.chiricahua or the other Madrean Sky Island taxa. These data provide the evolutionary framework for better understanding the region\'s complex biogeographic history (e.g., biotic assembly of the Chiricahua Mountains) and conservation of these spiders.

While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbA ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth-Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.

The Acorus calamus group, or sweet flag, includes important medicinal plants and is classified into three species: A. americanus (diploid), A. verus (tetraploid), and A. calamus (sterile triploid of hybrid origin). Members of the group are famous as components of traditional Indian medicine, and early researchers suggested the origin of the sweet flag in tropical Asia. Subsequent research led to an idea of the origin of the triploid A. calamus in the Amur River basin in temperate Asia, because this was the only region where both diploids and tetraploids were known to co-occur and be capable of sexual reproduction. Contrary to this hypothesis, triploids are currently very rare in the Amur basin. Here, we provide the first evidence that all three species occur in Kazakhstan. The new records extend earlier data on the range of A. verus for c. 1800 km. Along the valley of the Irtysh River in Kazakhstan and the adjacent Omsk Oblast of Russia, A. verus is recorded in the south, A. americanus in the north, and A. calamus is common in between. We propose the Irtysh River valley as another candidate for a cradle of the triploid species A. calamus. It is possible that the range of at least one parent species (A. americanus) has contracted through competition with its triploid derivative species, for which the Irtysh River floods provide a tool for downstream range expansion. We refine our earlier data and show that the two parent species have non-overlapping ranges of variation in a quantitative metric of leaf aerenchyma structure.

Fungi, including filamentous fungi and yeasts, are major contributors to global food losses and waste due to their ability to colonize a very large diversity of food raw materials and processed foods throughout the food chain. In addition, numerous fungal species are mycotoxin producers and can also be responsible for opportunistic infections. In recent years, MALDI-TOF MS has emerged as a valuable, rapid and reliable asset for fungal identification in order to ensure food safety and quality. In this context, this study aimed at expanding the VITEK® MS database with food-relevant fungal species and evaluate its performance, with a specific emphasis on species differentiation within species complexes. To this end, a total of 380 yeast and mold strains belonging to 51 genera and 133 species were added into the spectral database including species from five species complexes corresponding to Colletotrichum acutatum, Colletotrichum gloeosporioides, Fusarium dimerum, Mucor circinelloides complexes and Aspergillus series nigri. Database performances were evaluated by cross-validation and external validation using 78 fungal isolates with 96.55% and 90.48% correct identification, respectively. This study also showed the capacity of MALDI-TOF MS to differentiate closely related species within species complexes and further demonstrated the potential of this technique for the routine identification of fungi in an industrial context.

Understanding the dispersal potential of different species is essential for predicting recovery trajectories following local disturbances and the potential for adaptive loci to spread to populations facing extreme environmental changes. However, dispersal distances have been notoriously difficult to estimate for scleractinian corals, where sexually (as gametes or larvae) or asexually (as fragments or larvae) derived propagules disperse through vast oceans. Here, we demonstrate that generational dispersal distances for sexually produced propagules can be indirectly inferred for corals using individual-based isolation-by-distance (IbD) analyses by combining reduced-representation genomic sequencing with photogrammetric spatial mapping. Colonies from the genus Agaricia were densely sampled across plots at four locations and three depths in Curaçao. Seven cryptic taxa were found among the three nominal species (Agaricia agaricites, Agaricia humilis and Agaricia lamarcki), with four taxa showing generational dispersal distances within metres (two taxa within A. agaricites and two within A. humilis). However, no signals of IbD were found in A. lamarcki taxa and thus these taxa probably disperse relatively longer distances. The short distances estimated here imply that A. agaricites and A. humilis populations are reliant on highly localized replenishment and demonstrate the need to estimate dispersal distances quantitatively for more coral species.

DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information\'s nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

The trematodes are a species-rich group of parasites, with some estimates suggesting that there are more than 24,000 species. However, the complexities associated with their taxonomic status and nomenclature can hinder explorations of the biology of wildlife trematodes, including fundamental aspects such as host use, life cycle variation, pathology, and disease. In this chapter, we review work on selected trematodes of amphibians, birds, mammals, and their snail intermediate hosts, with the goal of providing a tool kit on how to study trematodes of wildlife. We provide a brief introduction to each group of wildlife trematodes, followed by some examples of the challenges each group of trematodes has relative to the goal of their identification and understanding of the biology and interactions these organisms have with their wildlife hosts.

The Canary Islands is a Macaronesian volcanic archipelago with a depauperate community of three species of Kalotermitidae, including Kalotermes dispar. A total of 54 Kalotermes colonies were collected from Gran Canaria, Tenerife, La Gomera, La Palma, and El Hierro islands. Soldiers and imagos were morphologically examined and sequenced for four mitochondrial markers. Although morphological differences could not be detected, phylogenetic analysis of both cox1/tRNA/cox2 and rrnL markers revealed two distinct clades of K. dispar, suggesting cryptic diversity. The diversification within the Canary Kalotermes lineage most likely occurred around 7.5 Mya, while the divergence within the two clades was reconstructed at about 3.6 Mya and 1.9 Mya. Kalotermes approximatus from the southeastern Nearctic constitutes a sister to the Canary Kalotermes, while the Palearctic K. flavicollis, K. italicus, and K. phoenicae form a separate clade. It is hypothesized that a faunal exchange of Kalotermes from the Nearctic to the Canary Islands occurred via transoceanic rafting during the mid-Miocene.

The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.