Nuclear Gene Research Articles

One-pot, degradable, silica nanocarriers with encapsulated oligonucleotides for mitochondrial specific targeting

Mutations in nuclear and mitochondrial genes are responsible for severe chronic disorders such as mitochondrial myopathies. Gene therapy using antisense oligonucleotides is a promising strategy to treat mitochondrial DNA (mtDNA) diseases by blocking the replication of the mutated mtDNA. However, transport vehicles are needed for intracellular, mitochondria-specific transport of oligonucleotides. Nanoparticle (NP) based vectors such as large pore mesoporous silica nanoparticles (LP) often rely on surface complexation of oligonucleotides exposing them to nucleases and limiting mitochondria targeting and controlled release ability. In this work, stable, fluorescent, hollow silica nanoparticles (HSN) that encapsulate and protect oligonucleotides in the hollow core were synthesized by a facile one-pot procedure. Both rhodamine B isothiocyanate and bis[3-(triethoxysilyl)propyl]tetrasulfide were incorporated in the HSN matrix by co-condensation to enable cell tracing, intracellular-specific degradation and controlled oligonucleotide release. We also synthesized LP as a benchmark to compare the oligonucleotide loading and release efficacy of our HSN. Mitochondria targeting was enabled by NP functionalization with cationic, lipophilic Triphenylphosphine (TPP) and, for the first time a fusogenic liposome based carrier, previously reported under the name MITO-Porter. HSN exhibited high oligonucleotide incorporation ratios and release dependent on intracellular degradation. Further, MITO-Porter capping of our NP enabled delayed, glutathione (GSH) responsive oligonucleotide release and mitochondria targeting at the same efficiency as TPP functionalized NP. Overall, our NP are promising vectors for anti-gene therapy of mtDNA disease as well as many other monogenic disorders worldwide.Graphical

Molecular and morphological evidence of hybridization between two dimorphic sympatric species of Fuchsia (Onagraceae).

Hybridization is commonly reported in angiosperms, generally based on morphology, and in few cases confirmed by molecular markers. Fuchsia has a long tradition of ornamental cultivars with different hybrids produced by artificial crosses, so natural hybridization between sympatric Fuchsia species could be common. Natural hybridization between F. microphylla and F. thymifolia was tested using six newly developed microsatellites for F. microphylla in addition to other molecular markers with codominant and maternal inheritance. Geometric morphometrics of leaves and floral structures were also used to identify putative hybrids. Hybrids showed a different degree of genetic admixture between both parental species. Chloroplast DNA (cpDNA) sequences indicated that hybridization occurs in both directions, in fact, some of the hybrids showed new haplotypes for cpDNA and ITS (internal transcriber spacer of nuclear ribosomal RNA genes) sequences. The morphology of hybrid individuals varied between the two parental species, but they could be better identified by their leaves and floral tubes. Our study is the first to confirm the hybridization in natural populations of Fuchsia species and suggests that hybridization has probably occurred repeatedly throughout the entire distribution of the species. Phylogeographic analysis of both species will be essential to understanding the impact of hybridization throughout their complete distribution.

A new Asian lazy toad of the genus Scutiger Theobald, 1868 (Anura, Megophryidae) from southern Tibet, China.

In this study, a new species named Scutigerluozhaensissp. nov. is described from Luozha, southern Tibet, China. Genetic analysis based on two mitochondrial genes 16S rRNA and COI and the nuclear gene RAG1 revealed that the new species belongs to an independent phylogenetic clade close to S.gongshanensis and S.nyingchiensis and shares no RAG1 haplotype with other species. Morphological comparisons based on examined specimens and literatures indicated that it can be diagnosed from congeners by the following combination of characters: (1) body moderate, male body length 47.0-67.2 mm (n = 13), female body length 49.8-66.2 mm (n = 8); (2) maxillary teeth and budding absent; (3) numerous tiny dense nuptial spines present on dorsal surface of fingers I, II and inner surface of finger III of males in breeding condition with similar size; (4) spine patches on belly of males in breeding condition absent; (5) spines on inner surface of forearm and upper arm of males in breeding condition absent; (6) small patches of black spines present near armpit of males in breeding condition absent; (7) adult males without vocal sac; (8) some large warts and tubercles on dorsum gathered into short skin ridges with several spines present on top; (9) space between upper eyelids wider than upper eyelids; (10) spots or irregular cross bands on limbs absent; (11) webbing between toes rudimentary; (12) coloration of dorsal body olive brown to bronze.

The nuclear receptor gene E75 plays a key role in regulating the molting process of the spider mite, Tetranychus urticae.

The nuclear receptor gene Ecdysone-induced protein 75 (E75), as the component of ecdysone response genes in the ecdysone signaling pathway, has important regulatory function for insect molting. However, the regulatory function of E75 during the molting process of spider mites is not yet clear. In this study, the expression pattern of E75 in the molting process of the spider mite Tetranychus urticae was analyzed. The results showed that there was a peak at 8h post-molting, followed by a decline 8h after entering each respective quiescent stage across various developmental stages. During the deutonymph stage, the expression dynamics of E75, observed at 4-h intervals, indicated that the transcript levels of TuE75 peaked at 24h, coinciding with the onset of molting in the mites. To investigate the function of TuE75 during the molting process, silencing TuE75 through dsRNA injection into deutonymph mites at the age of 8h yielded a notable outcome: 78% of the deutonymph mites were unable to progress to the adult stage. Among these phenotypic mites, 37% were incapable of transitioning into the quiescent state and eventually succumbed after a certain period. An additional 41% of the mites successfully entered the quiescent state but encountered difficulties in shedding the old epidermis, leading to eventual mortality. In summary, these results suggested that TuE75 plays a key role in the molting process of T. urticae.

Genome Editing of Plant Mitochondrial and Chloroplast Genomes.

Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria, yet they maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures and undergoing frequent homologous recombination. To date, it has proven to be challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene-editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially transcription activator-like effector nucleases (TALENs) and artificial enzymes utilizing DNA-binding domains of TALENs (TALEs), have been successfully used to modify these genomes by harnessing organellar-targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors in organellar genomes, their effects and their potential applications in plant science and breeding.

A TAXONOMIC REVISION OF THE MADAGASCAR-ENDEMIC GENUS BEMANGIDIA (SAPOTACEAE), WITH DESCRIPTION OF A SECOND SPECIES

Bemangidia L.Gaut. (Sapotaceae) is a genus endemic to a restricted area in the southeastern lowland moist evergreen forests of Madagascar. It was published in 2013 to accommodate an undescribed species, Bemangidia lowryi L.Gaut., which showed a combination of characters unique in the family Sapotaceae. At the time of description, three atypical collections from the same locality but growing on a ridge, slightly higher in altitude, were already known. Although matching well with the Bemangidia genus, they were phenotypically different from B. lowryi and were therefore not included in the species description. In the present study, we evaluate whether these specimens correspond to a new species, using a combination of morphological and genetic data based on 638 nuclear genes. The results show that Bemangidia contains two lineages, each one corresponding to a different morphology, with a genetic branch length similar to those observed among species pairs in other genera of Sapotaceae. We conclude that the genetic and morphological differences are sufficient to consider the two lineages as two distinct species. Consequently, the genus is here revised and a second species described.

Two independent LAMP assays for rapid identification of the serpentine leafminer, Liriomyza huidobrensis (Blanchard, 1926) (Diptera: Agromyzidae) in Australia

Liriomyza huidobrensis is a leafminer fly and significant horticultural pest. It is a quarantine listed species in many countries and is now present as an established pest in Australia. Liriomyza huidobrensis uses a broad range of host plants and has potential for spread into various horticultural systems and regions of Australia. Rapid in-field identification of the pest is critically needed to assist efforts to manage this pest. Morphological identification of the pest is effectively limited to specialist examinations of adult males. Generally, molecular methods such as qPCR and DNA barcoding for identification of Liriomyza species require costly laboratory-based hardware. Herein, we developed two independent and rapid LAMP assays targeted to independently inherited mitochondrial and nuclear genes. Both assays are highly sensitive and specific to L. huidobrensis. Positive signals can be detected within 10 min on laboratory and portable real-time amplification fluorometers. Further, we adapted these assays for use with colorimetric master mixes, to allow fluorometer free in-field diagnostics of L. huidobrensis. Our LAMP assays can be used for stand-alone testing of query specimens and are likely to be essential tools used for rapid identification and monitoring of L. huidobrensis.

Mito‐nuclear discordance and phylogeography of the surf clam Mesodesma donacium along the Southeast Pacific coast

AbstractMesodesma donacium is a surf clam endemic to the southeast Pacific coast, and it is an important resource species of the sandy beach artisanal fishery in Peru and Chile. Over time, the species has shown high variability in population dynamics (presence and abundance), which has been attributed to overfishing and environmental events. In this study, we assess the phylogeography of seven natural beds of M. donacium (17 to 42° S), to reveal the geographic distribution of the genetic diversity through the analysis of 278 sequences of the mitochondrial gene COI. Sequences of the nuclear genes 18S and 28S were used to evaluate the divergence of COI haplogroups. Two divergent parapatric mitochondrial haplogroups were found, which lacked divergence at nuclear markers (18S and 28S); this mito‐nuclear discordance allows inferring that there is no reproductive isolation of mitochondrial haplogroups. The North haplogroup is the only one present at the northernmost site, while only the South haplogroup was present in Cucao in the south. Between 28° and 32° S, coincident with a coastal biogeographic break at 30° S, both haplogroups are in sympatry. Haplogroups differed in their genetic structure, with the North haplogroup representing a single, highly diverse population and the South haplogroup with genetic differentiation and more restricted genetic diversity and gene flow. The divergence in mitochondrial haplogroups without nuclear divergence suggests a past scenario of geographic isolation in the northern and southern areas, without developing reproductive isolation, followed by secondary contact. Given the phylogeography, genetic information should be considered in restocking and management activities.

The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases.

Mitochondrial transcription factor A (TFAM) is a mitochondrial protein encoded by nuclear genes and transported from the cytoplasm to the mitochondria. TFAM is essential for the maintenance, expression, and delivery of mitochondrial DNA (mtDNA) and can regulate the replication and transcription of mtDNA. TFAM is associated with the formation of mtDNA nucleomimetic structures, mtDNA repair, and mtDNA stability. However, the mechanism by which TFAM protects mtDNA is still being studied. This review provides a summary of the protective mechanism of TFAM on mtDNA including the discrete regulatory effects of TFAM acetylation and phosphorylation on mtDNA, the regulation of Ca2+ levels by TFAM to activate transcription in mitochondria, and the increased binding of TFAM to mtDNA damage hot spots. This review also discusses the association between TFAM and some neurodegenerative diseases.

Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data.

Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.

Genetic, metabolic and clinical delineation of an MRPS23-associated mitochondrial disorder

MRPS23 is a nuclear gene encoding a mitochondrial ribosomal protein. A patient with a mitochondrial disorder was found to carry a variant in MRPS23. More cases are necessary to establish MRPS23 as a mitochondrial disease gene. Of 5134 exomes performed in our center, we identified five independent patients who had similar clinical manifestations and were homozygous for the same germline variant c.119C>T; p.P40L in MRPS23. Detailed clinical findings, mitochondrial enzyme activity assays from cultured skin fibroblasts, PCR-Sanger-sequencing, and variant age estimation were performed. Their available family members were also studied. Eight members homozygous for the MRPS23 p.P40L were identified. All were from Hmong hilltribe. Seven presented with alteration of consciousness and recurrent vomiting, while the eighth who was a younger brother of a proband was found pre-symptomatically. Patients showed delayed growth and development, hearing impairment, hypoglycemia, lactic acidosis, and liver dysfunction. In vitro assays of cultured fibroblasts showed combined respiratory chain complex deficiency with low activities of complexes I and IV. PCR-Sanger-sequencing confirmed the variant, which was estimated to have occurred 1550 years ago. These results establish the MRPS23-associated mitochondrial disorder inherited in an autosomal recessive pattern and provide insight into its clinical and metabolic features.

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

BackgroundDespite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana.ResultsOur pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments, and (4) the topology of the nuclear and plastid phylogenies. Additionally, the simulated reads derived from the genome of Arabidopsis thaliana were used to evaluate the accuracy and completeness of the recovered loci. In terms of computation time, locus recovery per sample, and informative sites, Captus outperforms HybPiper and SECAPR. The resulting topologies of Captus and SECAPR are identical for coalescent trees but differ when trees are inferred from concatenated alignments. The HybPiper phylogeny is similar to Captus in both methods. The nuclear genes recover a deep split of Thladiantha in two clades, but this is not supported by the plastid data.ConclusionsCaptus is the best choice among the three pipelines in terms of computation time and locus recovery. Even though there is no significant topological difference between the Thladiantha species trees produced by the three pipelines, Captus yields a higher number of gene trees in agreement with the topology of the species tree (i.e., fewer genes in conflict with the species tree topology).

A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor.

A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Gill Structure Linked to Ecological and Species Diversification in a Clade of Caddisflies

Streams represent a special case of directional environmental gradients where ecological opportunity for diversification may be associated with upstream and downstream dispersal into habitats that differ in selective pressures. Temperature, current velocity and variability, sediment erosion dynamics and oxygen saturation are key environmental parameters that change in predictable ways from springs to river mouth. Many aquatic insects occupy specific longitudinal regions along these gradients, indicating a high degree of adaptation to these specific environmental conditions. In caddisflies, the evolution of tracheal gills in larval and pupal stages may be a major driver in oxygen uptake efficiency and ecological diversification. Here we study the evolution of larval gill structure in the Rhyacophila vulgaris species group using phylogenomic methods. Based on anchored hybrid enrichment, we sequenced 97 kbp of data representing 159 independent nuclear protein coding gene regions to infer the phylogeny of the R. vulgaris species group, whose species exhibit both high diversity of gill types and varied longitudinal preferences. We find that the different gill types evolved independently as derived characters in the genus and that gill structure is linked to the longitudinal habitat preference, thereby serving as a possible ecological key innovation in the R. vulgaris group.

Redescription and Molecular Characterisation of Derogenes ruber Lühe, 1900 (Hemiuroidea: Derogenidae) from Chelidonichthys lastoviza (Scorpaeniformes: Triglidae) in the Western Mediterranean

PurposeDerogenes ruber Lühe, 1900, the type-species of the genus Derogenes Lühe, 1900, is a poorly known derogenid digenean. The original description of this species was not illustrated and aspects of the morphology of the parasite from the type-host remain scarce. Available records of this species were brief and/or lacked illustrations and were based on morphology alone. Additionally, molecular data for Derogenes spp. are warranted to untangle species complexes as they provide a better assessment of interspecific genetic divergence.MethodsDerogenes ruber is redescribed based on newly collected specimens from the gall bladder of its type-host Chelidonichthys lastoviza (Bonnaterre, 1788) collected in the Western Mediterranean off the Algerian coast during 2017–2019 and molecular data are provided using a partial fragment of the nuclear 28S ribosomal RNA gene (28S rRNA), the internal transcribed spacer 2 (ITS2) and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene.ResultsWe herein provide a detailed illustrated redescription and morphometric data of D. ruber from its type-host C. lastoviza. We report a new geographical record (off Algeria) for it. Derogenes ruber is also genetically characterised for the first time. Species/lineages of Derogenes were recovered in five strongly supported reciprocally monophyletic clades: (i) D. ruber from C. lastoviza off Algeria; (ii) D. lacustris from Galaxias maculatus (Jenyns) off Argentina; (iii) Lineage “D. varicus DV1” (D. varicus sensu stricto) from fish hosts in the White and Barents seas and the North Sea; (iv) Lineage “D. varicus DV2” from mollusc hosts in the White Sea; and (v) Lineage “D. varicus DV3” from Eumicrotremus fedorovi Mandrytsa. in the Pacific Ocean. Hence, comparison of the newly generated sequences with other available data for Derogenes species supports the distinction of D. ruber confirming its taxonomic status and helping assess interspecific variation. Comparison of D. ruber with the closely related species Derogenes latus revealed overlaps in morphometric data and the validity of the latter species is questioned.ConclusionThe combination of morphological and molecular data provided for D. ruber provides a firm foundation for further investigations of Derogenes spp. Although we do describe herein material of D. ruber from the type-host, given that the occurrence of a single Derogenes species in various hosts has been challenged by molecular data, and both D. lacustris and D. varicus sensu stricto had been genetically proven to occur in various hosts, D. ruber and D. latus may be indeed synonymous. Additional sequencing effort on Derogenes spp. will strengthen systematic comparative studies and evolutionary relationships within the Derogenidae in general.

Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec.

There is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported. Following a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of Ancyromonas sigmoides (Kent, 1881). The sequence of the mitogenome retrieved was 41,889 bp in length and encoded 38 protein-coding genes, 5 non-conserved open-reading frames, and 2 rRNA and 24 tRNA genes. The mitogenome has retained sdh2 and sdh3, two genes of the succinate dehydrogenase complex, which are sometimes found among basal eukaryotes but seemingly missing among the Malawimonadidae, a lineage sister to Ancyromonadida in some phylogenies. The phylogeny inferred from the 18S rRNA gene associated A. sigmoides from Sugluk Inlet with several other strains originating from the Arctic. The study also unveiled the presence of a metagenomic sequence ascribed to bacteria in GenBank, but it was clearly a mitochondrial genome with a gene content highly similar to that of A. sigmoides, including the non-conserved open-reading frames. After re-annotation, a phylogeny was inferred from mitochondrial protein sequences, and it strongly associated A. sigmoides with the misidentified organism, with the two being possibly conspecific or sibling species as they are more similar to one another than to species of the genus Malawimonas. Overall our phylogeny showed that the ice associated ancryomonads were clearly distinct from more southerly strains.

An investigation of large-leaved Gunnera L. (Gunneraceae) grown outside in Britain and Ireland

A molecular investigation of large-leaved Gunnera growing outside in Britain and Ireland was conducted. Two low-copy nuclear CYCLOIDEA-like genes (CYC-like 1 and CYC-like 2) and two chloroplast DNA regions (matK and psbD-trnT) were sequenced for 271 samples of Gunnera. While it was confirmed that genuine G. tinctoria is growing both in cultivation and in the wild, the results support recently published morphological and historical findings that the species G. manicata appears no longer to be present in Britain and Ireland. Instead, the plant under this name is G. × cryptica, a hybrid between G. manicata and G. tinctoria. The implication of this discovery for legislation on invasive non-native species where G. manicata and G. tinctoria are listed is explored.

A new species of shrew moles, genus Uropsilus Milne-Edwards, 1871 (Mammalia, Eulipotyphla, Talpidae), from the Wuyi Mountains, Jiangxi Province, eastern China.

Asian shrew moles, genus Uropsilus, are the most primitive members of family Talpidae. They are distributed mainly in southwestern China and adjacent Bhutan, Myanmar, and Vietnam. In June 2022, we collected five specimens of Uropsilus from Mount Huanggang, Jiangxi Province, eastern China, which is the highest peak of the Wuyi Mountains. We sequenced two mitochondrial (CYT B and 12S rRNA) and three nuclear (PLCB4, RAG1, and RAG2) genes to estimate the phylogenetic relationship of the five shrew moles. We also compared their morphology with recognized species within the genus. Our results show that these specimens collected from Mount Huanggang differ from all named species in Uropsilus. We formally describe the species here as Uropsilushuanggangensissp. nov. Morphologically, the new species is distinguishable from the other Uropsilus species by the combination of dark chocolate-brown pelage, long snout, enlarged first upper incisor, similarly sized lacrimal and infraorbital foramens, and the curved and sickle-like coronoid process. The genetic distances of the cytochrome b (CYT B) gene between U.huanggangensis and other recognized Uropsilus species ranged between 9.3% and 16.4%. The new species is geographically distant from other species in the genus and is the easternmost record of the Uropsilus. The divergence time of U.huanggangensis was estimated to be the late Pliocene (1.92 Ma, 95% CI = 0.88-2.99).

Molecular population genetics and phylogeographic studies of Ligia exotica and Ligia cinerascens in East Asia

IntroductionSea slater, in the genus Ligia, is widespread in rocky shore habitats, and the taxon is easily isolated due to its limited dispersal capacity. Therefore, most Ligia species exhibit an allopatric distribution, but Ligia exotica and L. cinerascens exhibit an overlapping distribution distribution in East Asia. Previous studies on both species have confirmed the existence of highly divergent lineages based on 16S rRNA.MethodsIn the present study, 282 Ligia individuals were collected at ten, three, and three sites in South Korea, Japan, and Vietnam, respectively, and 41 haplotypes were observed based on 16S rRNA.Results and discussionThe results of phylogeny, phylogenetic network, and TCS network, Principal Coordinates Analysis, and four Molecular Species Delimitation Analyses revealed that six genetic lineages including L. cinerascens, Lineages N and S of L. exotica, Ligia sp. 1, sp.2 and sp.3 were present. The three genetic lineages, including L. cinerascens, Lineage N of L. exotica, and Lineage S of L. exotica, were also identified in the phylogeny based on a nuclear gene of the sodium–potassium ATPase α-subunit (Nak). Phylogeographic analysis revealed that L. cinerascens and Lineage N of L. exotica were distributed overlappingly in South Korea, Japan, and the northern region of China. Generally, the two lineages of L. exotica were distributed allopatrically, which was more evident along the coastline of mainland China than that of Japan. The results of time-calibrated phylogeny suggested that the speciation events of Ligia species might be associated with Japanese mainland formation from Oligocene to Miocene (approximately 30-5 million years ago, Mya). The results of the present study provide insights that could facilitate the understanding of the evolutionary history of Ligia, tracking of geological processes, and evolutionary effects of palaeogeographical events at the population level.