Potential Cryptic Species Research Articles

Miamiensis avidus, a Novel Scuticociliate Pathogen Isolated and Identified from Cultured Large Yellow Croaker (Larimichthys crocea).

Scuticociliates are recognized as the causative agents of mass mortalities in certain cultured marine fishes, resulting in enormous economic losses. This study aimed to investigate a fatal infection caused by scuticociliates in farmed large yellow croaker (Larimichthys crocea) in Fujian province, China. Microscopic examinations of focal organs, including the brain, eyes, gills, and skin, revealed the presence of parasites. Active masses of scuticociliates were observed in these organs, and the ciliates were subsequently isolated and maintained in vitro. An immersion challenge experiment revealed that L. crocea experienced cumulative mortalities reaching 73% within 7 d upon exposure to 1.0 × 104 ciliates mL-1. Based on the microscopic and PCR testing of infected fishes, the brain was comprehensively inferred as the main infection organ for the isolated strain. Microscopic and submicroscopic observations of the isolated scuticociliate, coupled with cortical ciliature patterns revealed through α-tubulin indirect immunofluorescence techniques, identified these scuticociliates as Miamiensis avidus. The sequencing of two genetic markers (small subunit ribosomal RNA, SSU rRNA and cytochrome c oxidase subunit I, COI) further confirmed that the isolated strains exhibited the highest sequence similarity to most M. avidus sequences in GenBank. However, significant differences in SSU sequences compared to the M. avidus strain Ma/2, and the lack of published COI and ITS (internal transcribed spacer) sequences for Ma/2, indicate the need for further molecular data to resolve whether there are potential cryptic species within the M. avidus complex.

The State of the Art of the Global Distribution of the Invasive Mytilid Species Brachidontes pharaonis (P. Fischer, 1870)

The studies on the bioinvasion phenomenon focus mainly on the biological and ecological traits of a species, while scattered literature is addressed to a correct systematic assessment and an updated geographical distribution on the whole. It is noteworthy that non-indigenous species should be monitored on both sides of their range, i.e., towards the front of dispersal and beyond the original range. The backside range boundaries are not often monitored or well delimited; thus, the novel global distribution of an invasive taxon is not often accurately delimitated. A model species for highlighting criticisms about the scarce knowledge on the novel range was chosen. Brachidontes pharaonis is a mussel that has successfully colonised the Mediterranean Sea, following an immigration pathway through the Suez Canal from the Red Sea, presumably from a wider Indo-Pacific area. In this case, the Indo-Pacific boundaries have been overlooked and are still misunderstood due to diverse causes, principally as the synonymy with the congeneric B. variabilis has created confusion in the taxonomic identification. The present review demonstrates that the borders of the B. pharaonis range are still unclear and that the species should be analysed in a wider geographical area. Records of B. pharaonis from Southeast Asia should be treated with caution as this area is out of its range. The Indian and Pacific Oceans host the taxon B. variabilis, composed of two potential cryptic species. Data from the literature highlight the importance of the integrative taxonomic approach to solving various issues concerning the species group complex, morphological variations and cosmopolitan claims of species.

Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses.

The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.

Hidden hotspots of amphibian biodiversity in China

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

DNA Barcoding Supports "Color-Pattern''-Based Species of Stictochironomus from China (Diptera: Chironomidae).

The genus Stictochironomus (Diptera: Chironomidae) has an almost worldwide distribution, with more than 30 species. However, species delimitation and identification based on the markings on the wings and legs are controversial and uncertain. In this study, we focused on color patterns to review the adults of the genus from China, and two new species (S. trifuscipes sp. nov. and S. quadrimaculatus sp. nov.) are described and figured. DNA barcodes can accurately separate the two new species with specific color patterns. However, heterospecific individuals form a monophyletic cluster in the phylogeny tree. For example, S. maculipennis (Meigen) and S. pictulus (Meigen), which have a lower interspecific genetic divergence, form a single clade. Sequences with the same species name but with high intraspecific distance form more than one phylogenetic clade, such as S. sticticus (Fabricius) of three clades, S. pictulus of four clades, S. akizukii (Tokunaga) and S. juncaii Qi, Shi, and Wang of two clades, might have potential cryptic species diversity. Species delimitation analysis using ASAP, PTP, and GMYC clearly delineated them as separate species. Consequently, color patterns are a good diagnostic characteristic for species delimitation in Stictochironomus. The distance-based analysis shows that a threshold of 4.5-7.7% is appropriate for species delimitation in Stictochironomus. Additionally, an updated key including color pattern variation for male adults of known Stictochironomus species from China is provided.

Rhodophyta DNA Barcoding: Ribulose-1, 5-Bisphosphate Carboxylase Gene and Novel Universal Primers.

Red algae (Rhodophyta) are a heterogeneous group of marine algal species that have served as a source of high-value molecules, including antioxidants and scaffolds, for novel drug development. However, it is challenging to identify Rhodophytes through morphological features alone, and in most instances, that has been the prevailing approach to identification. Consequently, this study undertook the identification of red algae species in Kenton-on-Sea, South Africa, as a baseline for future research on red algae biodiversity and conservation. The identification was achieved by designing, analysing, and using a set of universal primers through DNA barcoding of the rbcL gene. The PCR products of the rbcL gene were sequenced, and 96% of the amplicons were successfully sequenced from this set and matched with sequences on BOLD, which led to these species being molecularly described. Amongst these species are medicinally essential species, such as Laurencia natalensis and Hypnea spinella, and potential cryptic species. This calls for further investigation into the biodiversity of the studied region. Meanwhile, the availability of these primers will ease the identification process of red algae species from other coastal regions.

Cryptic diversity and phylogeographic patterns of <italic>Plocamium telfairiae</italic> and <italic>P. cartilagineum</italic> (Plocamiales, Rhodophyta) in the Northwest Pacific

Cryptic diversity refers to two or more distinct species classified as a single species due to lack of morphological difference. Although Plocamium Lamouroux has potential applications in biotechnology, several phylogenetic studies suggest the presence of cryptic diversity within the genus that requires further phylogenetic evaluation. Here, we investigated two species of Plocamium, P. “cartilagineum” and P. “telfairiae”, in the Northwest (NW) Pacific. The aims of this study are to identify potential cryptic species by analyzing the genetic differences between the species from their type localities and specimens from the NW Pacific, to characterize their population genetic diversity and structure, and to find potential hotspots with high intraspecific genetic diversity in Korea. A reconstructed phylogenetic tree based on mitochondrial 5′ region of cytochrome c oxidase subunit I (COI-5P) and plastid ribulose-1,5-bisphosphate carboxylase / oxygenase large subunit (rbcL) with molecular delimitation methods revealed significant differences as distinct species in the genus Plocamium. Comparison with specimens from their type localities indicated the presence of two cryptic species in the NW Pacific, including Plocamium luculentum sp. nov. The phylogeographic study for both species showed low genetic differences among populations, demonstrating genetic connectivity within the NW Pacific. These findings could promote the discovery of other morphologically and ecologically similar but phylogenetically different Plocamium species worldwide, which is essential for conservation assessments.

Genomic evidence sheds new light on phylogeny of Rhabdophis nuchalis (sensu lato) complex (Serpentes: Natricidae)

Stable taxonomy and robust phylogeny are essential for the evolution and conservation of organisms. The Rhabdophis nuchalis (sensu lato) complex presently contains three species (R. nuchalis, R. chiwen, R. pentasupralabialis). Although several studies have explored the diversity and phylogeography of this group, certain issues related to systematics and taxonomy remain unresolved. Here, based on genome-wide data, including single nucleotide polymorphisms (SNPs) generated from ddRAD-seq and mitochondrial DNA (mtDNA), we re-evaluated the phylogenetic relationships and cryptic diversity of this species group. Our results are generally consistent with previous studies but provide some new insights. Phylogenetic relationship reconstruction based on SNPs and mtDNA revealed that three species in the R. nuchalis (sensu lato) complex did not form a monophyly but each species is well supported as monophyletic lineage in SNP-based analyses. Population structure analyses showed genetic admixture between several species pairs. Additionally, the population in eastern Yunnan, China, was identified as a potential cryptic species and thus described as a new species based on morphological data. From our results and previous studies, we redefined the distribution boundary for each species in the R. nuchalis (sensu lato) species complex.

Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications

Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.

Boring bryozoans: an investigation into the endolithic bryozoan family Penetrantiidae

An endolithic lifestyle in mineralized substrates has evolved multiple times in various phyla including Bryozoa. The family Penetrantiidae includes one genus with ten extant and two fossil species. They predominantly colonize the shells of molluscs and establish colonies by chemical dissolution of calcium carbonate. Based on several morphological characters, they were described to be either cheilostome or ctenostome bryozoans. For more than 40 years, neither the characters of species identity and systematics nor the problem of their phylogeny was approached. Consequently, the aim of this study is to reevaluate species identities and the systematic position of the genus Penetrantia by analyzing at least six different species from eight regions with the aid of modern methods such as confocal laser scanning microscopy and 3D-reconstruction techniques. This study demonstrates that the musculature associated with the operculum and brood chamber shows significant differences from the cheilostome counterparts and seems to have evolved independently. Together with the presence of other ctenostome-like features such as true polymorphic stolons and uncalcified body wall, this finding supports a ctenostome affinity. Operculum morphology reveals many new species-specific characters, which, together with information about gonozooid morphology, tentacle number, and zooid size ranges, will enhance species identification. It also revealed a probable new species in Japan as well as potential cryptic species in France and New Zealand. In addition, this study increases the known distribution range of the family and its substrate diversity. Altogether, the new information collated here provides the basis for future work on a neglected taxon.

Tragopogon pratensis: Multiple introductions to North America, circumscription, and the formation of the allotetraploid T. miscellus

AbstractTragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and T. miscellus, both of which formed in western North America following the human‐mediated introduction of three diploids from Europe: T. dubius, T. porrifolius, and T. pratensis. We recently investigated the genetics of the introduction history to North America of T. dubius, the shared parent of both allopolyploids. Here, we investigate the introduction of T. pratensis into North America, the second diploid parent of T. miscellus. Using ITS sequence data, we found that T. pratensis as currently defined in the narrow sense is polyphyletic and comprises at least four different major ITS types in its native range. Of these native range ITS patterns, two have been introduced from Europe into North America and now occur widely across Canada and the U.S.A. Although the allotetraploid T. miscellus formed multiple times in western North America, only one of these ITS types was involved in the recurrent formations. These results for T. pratensis parallel our findings for T. dubius and further suggest that not all genotypes of these two species may be able to participate in the formation of allopolyploids. Our phylogenetic analyses reveal that several entities traditionally considered part of T. pratensis in the narrow sense are genetically distinct and mark unique lineages that may ultimately merit recognition as separate species. This proclivity for genetically distinct entities (potential cryptic species) within species recognized based on morphology appears common in Tragopogon. To unravel the complexities of what is referred to as “T. pratensis”, more intensive phylogenetic analyses involving many more samples from across the geographic range of the species are required, as are detailed assessments of taxonomy, morphology, and cytology.

Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species.

Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.

Molecular phylogeny of the snorkel snail Rhiostoma housei, a species complex from Thailand with descriptions of three new species

Snorkel snails (genus Rhiostoma) are widely distributed in Indo-China and on the Malay Peninsula. The shell morphology is traditionally used for species identification yet in Thailand, the common snorkel snail, Rhiostoma housei, shows considerable variation in shell morphology within and between populations. Therefore species identifications and delimitations are difficult. We used two mitochondrial DNA fragments (COI and 16S rRNA) and morphological characters to delimit species and infer phylogenetic relationships of Rhiostoma housei s.l. from eight localities in Thailand, representing potential cryptic species suggested by earlier allozyme and karyological data. Results revealed four distinct clades from different geographic areas in Thailand. Species delimitation analyses confirmed the clades as four separate species and a geometric morphometric analysis demonstrated subtle but consistent conchological differences between the four clades. The high COI sequence divergences among the four clades (mean: 14.8%; range: 10.3–16.5%) further supported the species level recognition. As a consequence, three new species are described from Thailand: R. khoratense, sp. nov., R. nakwangense, sp. nov. and R. phunangense, sp. nov. ZooBank: urn:lsid:zoobank.org:pub:EE534749-9346-4972-BF2E-3B5D0EB8AED8

Photographic Checklist, DNA Barcoding, and New Species of Sea Slugs and Snails from the Faafu Atoll, Maldives (Gastropoda: Heterobranchia and Vetigastropoda)

Baseline biodiversity data are key for ecological and evolutionary studies and are especially relevant for areas such as the Maldivian Archipelago in the Indian Ocean, which can act as a stepping-stone for the transport of widely distributed marine species. We surveyed the islands and reefs of the Faafu and Malé Atolls with snorkeling and scuba diving, collecting the two gastropod subclasses, Heterobranchia and Vetigastropoda. Our inventory comprises 104 species photographed alive to create an identification guide. We also provide COI barcodes for most species, adding novel sequence data for the Maldivian malacofauna. Half of our species represent new records for the Maldives, emphasizing how much diversity remains to be discovered. Species distributions reflect ecological rarity, with almost 60% of taxa only found in one site. We also compiled a comprehensive checklist of heterobranchs and vetigastropods of the Maldives based on literature records, resulting in 320 species, which, together with barcoding data, indicate several potential cryptic species in the Indo-Pacific. Six new species are described, the nudibranchs Limenandra evanescenti n. sp., Eubranchus putnami n. sp., Sakuraeolis marhe n. sp., Moridilla maldivensis n. sp., Tergiposacca perspicua n. sp., and the sacoglossan Costasiella fridae n. sp.

South(East) by Southwest: Identification of a New Halocaridina rubra Holthuis, 1963 (Decapoda: Atyidae) Genetic Group From O‘ahu, Hawai‘i

The anchialine ecosystem, comprised of coastal landlocked habitats containing brackish water, experiences tidal fluctuations due to simultaneous underground connections with the sea and terrestrial aquifer system. Anthropogenic impacts have led to substantial habitat degradation and loss, potentially making the anchialine ecosystem and its biota one of Hawai‘i’s most threatened. Prior analyses of mitochondrial (mtDNA) cytochrome oxidase subunit I (COI) sequences from the Hawaiian anchialine atyid shrimp Halocaridina rubra revealed a potential cryptic species complex with strong regional endemism. This study hypothesized that a Halocaridina population discovered in 2018 in southeast O‘ahu, an area with no historically documented anchialine habitats but where a specimen was collected in 1998, represents a unique lineage or genetic group endemic to the region. Comparison of newly generated mtDNA COI sequences to previous ones identified the population as belonging to the South O‘ahu lineage of Halocaridina. However, fixed mutations and significant genetic differentiation distinguish it from the closely related ‘Ewa genetic group of southwest O‘ahu. Given this, we propose the new Maunalua genetic group for Halocaridina from southeast O‘ahu, with an apparent split between groups occurring at approximately the Holocene-Pleistocene Epoch boundary, corresponding well to the geological age of where the new population was discovered. Notably, the 1998 specimen shared the same distinctive coloration as the Maunalua and ‘Ewa genetic groups, implying inclusion within the South O‘ahu lineage. Conservation efforts should consider the currently recognized 15 Halocaridina genetic groups since they represent unique units from all others in both their genetics and geographic distribution.

Unravelling the Diversity of Microorganisms in Ticks from Australian Wildlife.

Ticks and tick-borne pathogens pose a significant threat to the health and welfare of humans and animals. Our knowledge about pathogens carried by ticks of Australian wildlife is limited. This study aimed to characterise ticks and tick-borne microorganisms from a range of wildlife species across six sites in Victoria, Australia. Following morphological and molecular characterisation (targeting 16S rRNA and cytochrome c oxidase I), tick DNA extracts (n = 140) were subjected to microfluidic real-time PCR-based screening for the detection of microorganisms and Rickettsia-specific real-time qPCRs. Five species of ixodid ticks were identified, including Aponomma auruginans, Ixodes (I.) antechini, I. kohlsi, I. tasmani and I. trichosuri. Phylogenetic analyses of 16S rRNA sequences of I. tasmani revealed two subclades, indicating a potential cryptic species. The microfluidic real-time PCR detected seven different microorganisms as a single (in 13/45 ticks) or multiple infections (27/45). The most common microorganisms detected were Apicomplexa (84.4%, 38/45) followed by Rickettsia sp. (55.6%, 25/45), Theileria sp. (22.2% 10/45), Bartonella sp. (17.8%, 8/45), Coxiella-like sp. (6.7%, 3/45), Hepatozoon sp. (2.2%, 1/45), and Ehrlichia sp. (2.2%, 1/45). Phylogenetic analyses of four Rickettsia loci showed that the Rickettsia isolates detected herein potentially belonged to a novel species of Rickettsia. This study demonstrated that ticks of Australian wildlife carry a diverse array of microorganisms. Given the direct and indirect human-wildlife-livestock interactions, there is a need to adopt a One Health approach for continuous surveillance of tick-associated pathogens/microorganisms to minimise the associated threats to animal and human health.

DNA barcoding and phylogenetic analysis of midges belonging to Culicoides (Diptera: Ceratopogonidae) subgenus Hoffmania in Yunnan, China

• Cox1 and 28S data were prepared from 6 species of C. ( Hoffmania ) in China. • Report 9 novel cox1 barcodes (BINs) for species of C. ( Hoffmania ). • Four species placed into Avaritia in China were transferred into Hoffmania . • Cryptic species were identified within C. innoxius, C. liui and C. insignipennis . • Two species are formally synonymised. DNA barcodes obtained from cytochrome c oxidase subunit 1 ( cox1 ) offer a fast and easy way to identify a range of biological organisms. Culicoides (Diptera: Ceratopogonidae) are a group of small, blood sucking midges whose species are the vectors for some arboviruses, such as bluetongue virus, African horse sickness virus, epizootic hemorrhagic disease virus and equine encephalosis virus. Identification of these small insects is difficult so constructing DNA barcode libraries for species present in certain areas is helpful to clarify the taxonomy and assist non-specialist workers to identify species. In this study, we analysed specimens belonging to C. subgenus Hoffmania collected from 12 towns of Yunnan Province, China. Specimens were identified by morphology and processed to construct DNA barcodes. A total of 185 specimens referable to 6 morphological species were processed for cox1 and 28S rRNA sequencing. The resulting 185 cox1 sequences were assigned to 13 barcode index numbers (BINs) which include 9 novel BINs. Molecular and morphological evidence was used to support the transfer of 4 species previously assigned to C. subg. Avaritia into C. subg. Hoffmania . Molecular analysis revealed the presence of 7 potential cryptic species within C. innoxius, three within C. liui and two within C. insignipennis .

Prevalence, Infection Intensity and Molecular Diagnosis of Mixed Infections with Metastrongylus spp. (Metastrongylidae) in Wild Boars in Uzbekistan.

The aim of the present study was to characterize the diversity of Metastrongylus spp. in wild boars and the earthworm intermediate host species contributing to the maintenance of the life cycle. Here, wild boars were subjected to parasitological necropsies, and lungworm species were identified morphologically, followed by confirmation using ITS-2 sequencing and a phylogenetic analysis. Earthworms were collected from wild boar habitats and investigated for the presence of larvae. The prevalence of Metastrongylus spp. in wild boars was 78.8%, and many individuals were positive for all three detected species, Metastrongylus pudendotectus, Metastrongylus salmi and Metastrongylus elongatus. The phylogenetic analysis did not clearly resolve all species, except for M. pudendotectus. Age group and season had no influence on prevalence, while intensity was significantly higher in autumn than in spring and summer (Kruskal-Wallis followed by Dunn's test). Three out of six investigated earthworm species were positive for metastrongyloid larvae (prevalence of 10.4-16.7%), but neither their phylogenetic relationship nor ecological microhabitats were able to explain these differences. Further sequence data should be used to improve the resolution in phylogenetic trees to determine potential cryptic species in the genus, while the application of deep sequencing approaches might provide insights into species-specific epidemiology and pathology.

The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera)

BackgroundFamily Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia–Oriental–Oceania (AOO) and Afrotropical–Madagascar–Palearctic (AMP)].ResultOur result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene.ConclusionOverall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.

The Genetic Diversity in Thereuonema tuberculata (Wood, 1862) (Scutigeromorpha: Scutigeridae) and the Phylogenetic Relationship of Scutigeromorpha Using the Mitochondrial Genome.

Simple SummaryThe sequencing of mitochondrial genomes promotes the study of cryptic species and the phylogenetic relationship of species. Thus far, only one complete mitochondrial genome of Scutigeromorpha is available in the NCBI. In this study, four specimens of Thereuonema tuberculata (Scutigeromorpha: Scutigeridae), collected from four different localities of China, were identified, and the four mitochondrial genomes of those were sequenced and annotated. Based on the gene organization and genetic diversity of the mitochondrial genomes, we hypothesized that cryptic species could exist in T. tuberculata. We further constructed BI and ML phylogenetic trees to reveal the relationship of Scutigeromorpha.Based on morphological characteristics to make species identification, the cryptic species of the Scutigeromorpha can be greatly underestimated. The mitochondrial genome provides a desirable tool for the biological identifications and the discovery of the cryptic species. The capacity to acquire mitochondrial genome sequences has substantially improved in recent years using next-generation sequencing (NGS) technology. On the basis of the next-generation sequencing, we obtained four complete mitochondrial genomes of Thereuonema tuberculata (Wood, 1862) from Nanyang, Henan Province (NY), Nanchang, Jiangxi Province (NC), Jinan, Shandong Province (JN), and Dali, Yunnan Province (DL) in China with GenBank numbers OK513221, OL449685, ON058988 and ON058989, respectively. The lengths of the four mitochondrial genomes ranged from 14,903 to 14,909 bp. The composition and order of genes of the four mitochondrial genomes were identical to the published mitochondrial genome of Scutigera coleoptrata (Linnaeus, 1758) (Scutigeromorpha: Scutigerdae). It was the first time that the tandem repeats in the control region were detected in Scutigeromorpha. We also calculated the corrected pairwise genetic distance of four complete mitochondrial genomes of T. tuberculata, ranging from 7.7 to 15.2%. The results showed that the T. tuberculata NC belonged to the typical sample of T. tuberculata, and T. tuberculata DL was hypothesized as a cryptic species of T. tuberculata. Meanwhile, T. tuberculata NY and T. tuberculata JN were hypothesized as potential cryptic species of T. tuberculata in this study. In both BI and ML trees, the monophyly of Scutigeromorpha, Scolopendromorpha, Geophilomorpha, and Lithobiomorpha was forcefully advocated. Moreover, Scutigeromorpha was recovered as the sister clade of (Scolopendromorpha + (Lithobiomorpha + Geophilomorpha)). Four specimens of T. tuberculata were clustered into one clade, which was the sister to the clade of S. coleoptrata.