ABSTRACT In recent years, a wide array of tools originally developed for molecular dating analyses has been adapted for use within a morphological clock perspective. This is of paramount relevance for taxonomic groups that cannot be sampled in forms suitable for DNA extraction. The Scolebythidae, a small family of stinging wasps, represents an interesting group to study the application of the morphological clock due to their limited extant diversity contrasted with their abundant Cretaceous fossil record. Here, we investigate the impact of model specifications on the Bayesian inference of dated phylogenetic trees for the family. A total of 78 models were evaluated through Bayes Factors, with a thorough comparison of topology and node ages across the resulting trees. We find that the partitioning of characters had slight effects on ages retrieved, even though partitioning by homoplasy improved model fit and yielded narrower ranges for age estimates. The uniform tree prior consistently provided older age estimates compared to the fossilised birth‐death prior. Models employing an Independent Gamma Rates (IGR) clock and lognormally distributed rate resulted in higher marginal likelihood values. While calibration priors had limited impact, the root age prior substantially affected both the estimates and overall model performance. We discuss the evolutionary history and biogeography of Scolebythidae, highlighting the relevance of dispersal events in shaping their modern disjunct distribution. Advances in the application of the morphological clock may be essential for bridging the extant diversity with the ever‐growing fossil record.

ABSTRACT The flatfish family Bothidae comprise 170 currently recognised species in 20 genera, classified under two subfamilies. Although previous morphological and molecular studies have supported the monophyly of the family, its intrafamilial relationships remain largely unexplored, and the monophyly of the 20 existing genera has yet to be thoroughly evaluated. This study aims to address these long‐standing systematic issues, particularly at the generic level, and to elucidate the sister‐group relationships within Bothidae using a comprehensive set of samples of 87 morphospecies across 19 genera, and DNA sequence data from two mitochondrial and three nuclear gene markers. Our results reveal that the subfamily Bothinae is paraphyletic with respect to monophyletic Taeniopsettinae. Additionally, ‘Bothinae’ can be subdivided into three main clades (Bothinae 1–3). At the generic level, while Grammatobothus is resolved as monophyletic (=Bothinae 1) and as the sister group to the remaining bothids, four other specious genera— Arnoglossus , Laeops , Parabothus , and Psettina —are not. To resolve these taxonomic inconsistencies, we integrate evidence from phylogeny, morphology, and biogeography. Consequently, we propose elevating Taeniopsettinae to family status, establishing two new families—Monolenidae (=Bothinae 2) and Grammatobothidae—each comprising a single genus, and restricting the family Bothidae to Bothinae 3. We also refine the usage of the valid generic names Arnoglossus (= Arnoglossus V), Laeops (= Laeops II), Parabothus (= Parabothus III), and Psettina (= Psettina III), and recommend the resurrection of previously synonymised bothid genera as well as the establishment of new genera. These taxonomic revisions are ongoing and will be elaborated upon in a forthcoming study.

ABSTRACTThe rapid climatic fluctuations and geographical factors during the Quaternary glacial period, particularly in the Pleistocene epoch, play a pivotal role in shaping intraspecific genetic diversity. We conducted an investigation into the genetic structure and speciation mechanisms of a small mammal species, Asiatic Short‐Tailed Shrew (Blarinella quadraticauda), which is mainly distributed in the mountains surrounding the Sichuan Basin and its adjacent regions in southwest China. Extensive sampling was conducted across the region (180 Asiatic Short‐Tailed Shrews from 67 sites), followed by principal component analysis and discriminant analysis on complete skull data. Phylogenetic analyses were conducted using mitochondrial (Cytb) and nuclear (APOB and BRCA1) genes. Additionally, the potentially suitable distribution range under both current and historical climatic conditions was projected. Our results show that B. quadraticauda in the Sichuan Basin is divided into six major clades, which are largely morphologically similar, except for the clade from Baoxing, Sichuan, which exhibits a slightly larger size. Additionally, the species exhibits a nearly ring‐like distribution around the Sichuan Basin. Genetic exchange among populations in the northern and eastern regions of the basin appears to be limited, suggesting potential barriers to gene flow. Under the influence of the basin's lowlands, the rapid climate oscillation of the Quaternary glacial period and the uplift of the Tibetan Plateau, the species appears to have formed a ring distribution in the Sichuan Basin. Moreover, we have also updated the taxonomy and distribution range of B. quadraticauda.

ABSTRACTThe present study evaluated the phylogenetic relationships among the six valid species of catfish of the genus Hypophthalmus, estimated the divergence times among the different taxa and assessed the processes that influenced the evolution of the group. All the phylogenetic analyses, based on 6803 base pairs, including three mitochondrial and seven nuclear markers, support the monophyly of Hypophthalmus, and the arrangement of the species in two clades, one containing Hypophthalmus oremaculatus + Hypophthalmus donascimientoi, and the other, including Hypophthalmus marginatus + Hypophthalmus edentatus, which is the sister group of Hypophthalmus celiae, with Hypophthalmus fimbriatus appearing as the most divergent of this clade. These findings indicate that the genus originated some 4.4 million years ago (Ma), during the Pliocene, while most species diversified during the Pleistocene. The origin and diversification of Hypophthalmus coincided with the formation of the modern Amazon basin and the climatic fluctuations of the Plio‐Pleistocene, which likely determined modifications in the dynamics of the local rivers and influenced the evolution and diversification of the genus.

ABSTRACTThe Qinghai‐Tibetan Plateau and Himalayas (QTPH) are biodiversity hotspots crucial for understanding alpine speciation. While studies have focused on flora and aboveground fauna, the impact of QTPH uplift on soil fauna diversification remains understudied. To address this research gap, we investigated a representative taxon of alpine soil animals, the Isotoma quadridentata species complex (Collembola, Isotomidae) widespread at 2300–5100 m above sea level across the QTPH. On a molecular aspect, we sequenced 2 mitochondrial (COI, 16S) and 3 nuclear (18S, 28S D1–2, 28S D7–10) markers from 79 individuals representing different populations of this complex and related species. Based on these data, our single‐locus (ABGD, ASAP) and multi‐locus (single‐rate and multi‐rate mPTP) species delimitation analyses supported 11–15 candidate species among this complex. On a morphological aspect, colour patterns varied both between and within the candidate species, suggesting caution in their use for Isotoma diagnosis. Macrochaetotaxy was largely consistent, except in AG4, which showed a distinct pattern on the head. Macroevolutionary analyses indicated a Himalayan origin for QTPH Isotoma 5.88–10.25 million years ago (Mya), with the I. quadridentata complex originating in the adjacent Emei Mountain later. This complex diversified initially in the Emei Mountain before dispersing to the northeast QTPH and back to Himalayas 3.82–6.48 Mya, followed by further speciation. These findings link the origin and diversification of QTPH Isotoma and the I. quadridentata complex to the uplift of the QTPH and subsequent environmental changes since Miocene, supporting a potential impact of this geological event on the diversification of alpine soil fauna.

ABSTRACTThe phylum Acanthocephala is a ubiquitous group of zooparasites, with major socio‐economic importance. The true diversity of the Acanthocephala is obscured by the phenomena of cryptic speciation and a large degree of intraspecific variation. In this study we describe an example of extreme phenotypic variation in neck morphology. The pomphorhynchid acanthocephalans, Longicollum pagrosomi and Pomphorhynchus zhoushanensis were originally differentiated on the basis of differences in neck morphology; P. zhoushanensis possesses a neck bulb whereas this structure is absent in L. pagrosomi. However, ASAP and phylogenetic analyses of the ITS, 12S, cox1 and cox2 sequence data, together with comparative mitogenomics, revealed that the two taxa are in fact conspecific. Therefore, the presence or absence of a neck bulb represents extreme phenotypic variation, and this character is not reliable for distinguishing the genera Pomphorhynchus and Longicollum. In the absence of other characters to discriminate the two genera, Longicollum is relegated to a junior synonym of Pomphorhynchus. A new combination Pomphorhynchus pagrosomi (Yamaguti, 1935) comb. nov. is proposed for L. pagrosomi Yamaguti, 1935 and P. zhoushanensis Li, Chen, Amin & Yang, 2017 is relegated to a junior synonym of P. pagrosomi.

ABSTRACTThe diversification of Neotropical sigmodontine rodents represents one of the most remarkable evolutionary events among mammals, encompassing numerous endemic, rare, and endangered genera and species. One of the most emblematic examples is Microakodontomys transitorius Hershkovitz 1993, originally described from a single specimen based on morphological traits, and considered a “transitional” taxon between the tribes Akodontini and Oryzomyini, due to its unique combination of characters. However, the lack of additional specimens and its morphological resemblance to small species of Oligoryzomys led to its taxonomic synonymization with that genus. Here, we report new karyological, morphological, and natural history information on this taxon, and present results of total evidence phylogenetic analyses of the tribe Oryzomyini. Cytogenetic analyses revealed two distinct karyotypes: a female with 2n = 38, FNa = 46, and a male with a mosaic 2n = 36–37, FNa = 44–45. Phylogenetic analyses integrating morphological, mitochondrial (cytochrome b), and nuclear (IRBP) data support the placement of M. transitorius within the Oryzomyini, but distinct from Oligoryzomys, and as a sister taxon to Lundomys molitor. We redescribe the taxon, discuss its phylogenetic relationships, and the implications of its diversification within the Cerrado biome.

Abstract The India‐Eurasia continental collision and the subsequent uplift of the Qinghai‐Tibet Plateau have profoundly influenced the diversification and endemism of aquatic organisms across Asia. Notably, the freshwater razor clam genus Novaculina, previously the sole known freshwater member of the family Pharidae, originally comprised four species distributed across Asia. Among these, the protected Chinese endangered species N. chinensis, with fused syphons and unclear taxonomic status, has drawn conservation and scientific focus. The recent reclassification of N. siamensis into the new genus Cenonovaculina highlighted the fused syphons of N. chinensis as a shared morphological trait; however, further investigation is needed to determine whether N. chinensis should be recognised as a distinct genus. Moreover, the phylogenetic relationships and biogeographic history of Novaculina sensu lato and its allied genera remain elusive, particularly given the limited molecular data available for the endangered Chinese species N. chinensis. In this study, we analysed newly collected specimens of N. chinensis from the Yangtze and Pearl River Basins, compiling genetic datasets that include three genes (COI, 16S rRNA, and 28S rRNA) as well as whole mitochondrial genome data. High‐throughput sequencing revealed no mitogenome heteroplasmy in somatic and male gonadal tissues, confirming the absence of doubly uniparental inheritance in N. chinensis. Our phylogenetic analyses revealed that Novaculina chinensis does not cluster with either Novaculina congeners or Cenonovaculina. Instead, these results robustly support the polyphyletic nature of Novaculina s.l., identifying N. chinensis as a relic marine‐derived freshwater lineage. We therefore erect Uninovaculina gen. nov. for N. chinensis. Our results also indicate that the subfamily Pharellinae originated from a saline habitat approximately 77.2 million years ago (95% HPD = 65.3–91.2). These findings highlight the critical influence of geological and climatic changes on the distribution of freshwater razor clams in Asia, underscoring the complex interplay between these factors and adaptive evolutionary processes.

Abstract Five stink bugs, Aelia acuminata, A. fieberi, A. furcula, A. klugii and A. sibirica, are found in China and have similar morphologies. Due to the lack of molecular data, the species boundaries and phylogenetic relationships among these five species remain uncertain. In this study, we integrated mitochondrial DNA and nuclear single nucleotide polymorphisms (SNPs) generated by double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) to perform species delimitation and phylogenetic analyses of the five Aelia species. Most species delimitation analyses based on the cytochrome c oxidase subunit I (COI) gene, mitochondrial genomes and nuclear SNPs yielded five molecular operational taxonomic units (MOTUs), which correspond well to the five Aelia species identified based on morphological characters. We obtained a clear mito‐nuclear discordance between the tree topologies based on mitochondrial genome and genome‐wide SNP data. The D‐statistic and TreeMix analysis suggested that introgression is the most likely cause of mito‐nuclear discordance in Aelia species, which requires confirmation through more extensive sampling and comprehensive data. This study provides the first molecular evidence of the species boundaries and phylogenetic relationships of these five Aelia stink bugs, which is crucial to our understanding of the biodiversity and evolution of Aelia species.

Abstract Stripes and bands are common colour patterns in snakes. Some species are known to exhibit colour polymorphism and that includes expressing it in the bands and stripes. Bridal snake, Dryocalamus is a medium‐sized arboreal snake in South to Southeast Asia and most species of the genus are banded, but including two striped species. In Borneo, banded D. subannulatus and striped D. tristrigatus occur sympatrically and the two species are similar morphologically except for their colour patterns. We hypothesized the two species in Borneo exhibit a significant colour dimorphism of one species and conducted morphological and genetical analysis to test the hypothesis. Morphological examinations revealed that D. subannulatus and D. tristrigatus are not distinguishable in Borneo by scalation. Mitochondrial phylogenetic analysis and nuclear SNP analysis showed D. subannulatus and D. tristrigatus from Borneo formed clades or clusters by region not by species. Dryocalamus subannulatus and D. tristrigatus in Borneo are morphologically and genetically indistinguishable and Bornean D. subannulatus should be treated as a colour morph of D. tristrigatus. This is a rare example of sympatrically distinct banded/striped dimorphism in snakes. Relative abundance of banded/striped morph of the genus is probably different depending on region, and any ecological factor may contribute to it.