Divergence time of mites of the family Laelapidae based on mitochondrial barcoding region

Using the mitochondrial barcoding region to correlate research with 58 species in 19 genera of the family Laelapidae with the aim of determining the origin, phylogenetic relationships, and biogeographic historical distribution characteristics of mites in the family Laelapidae. Phylogenetic trees were obtained using Bayesian inference (BI) and Maximum-likelihood (ML) methods, based on three fossil records calibrated as molecular clock nodes, to estimate the divergence time of mites in the family Laelapidae as well as to apply Dispersal-Extinction-Cladogenesis (DEC) analyses to obtain biogeographic history inferences. The result showed species of the genera Hyperlaelaps and Haemolaelaps and some species of the genus Androlaelaps in the family Laelapidae were divided into clades of the genus Laelaps in both the BI and ML trees. Divergence time estimates and biogeographic history analysis revealed that the family Laelapidae likely diverged from other taxa during the Middle Jurassic (ca. 156.73 Mya), with Asia considered the most likely ancestral region for the family Laelapidae. Species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The results suggest that some genera in the family Laelapidae need to be re-defined or new genera need to be established; the Late Cretaceous to Late Neogene warm period would have promoted the divergence and expansion of species in the family Laelapidae. The divergence and dispersal of the family Laelapidae species is most likely a joint response to the continued northward drift of the Indian plate away from the Gondwana paleo-continent and gradually closer to Asia during the Late Cretaceous and the geological activity of the Tibetan Plateau during the Cenozoic Tertiary. The results strengthen our understanding of the origin and evolution of species in the family Laelapidae.

Morphological Identification and Phylogenetic Analysis of Laelapin Mite Species (Acari: Mesostigmata: Laelapidae) from China

Laelapinae mites are involved in transmission of microbial diseases between wildlife and humans, with an impact on public health. In this study, 5 mite members in the subfamily Laelapinae (laelapin mites; LM) were morphologically identified by light microscopy, and the phylogenetic relationship of LM was analyzed in combination with the sequence information of part of the LM cytochrome oxidase subunit I (cox1) gene. The morphological identification revealed that 5 mites belonged to the genera Laelaps and Haemolaelaps, respectively. Sequence analysis showed that the ratio of non-synonymous mutation rate to synonymous mutation rate of LM was less than 1, indicating that the LM cox1 gene had undergone purifying selection. Phylogenetic analysis showed that the Laelapinae is a monophyletic group. The genera Haemolaelaps and Hyperlaelaps did not separated into distinct clades but clustered together with species of the genus Laelaps. Our morphological and molecular analyses to describe the phylogenetic relationships among different genera and species of Laelapinae provide a reference for the improvement and revision of the LM taxonomy system.

Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.

A DNA barcode library for mangrove gastropods and crabs of Hong Kong and the Greater Bay Area reveals an unexpected faunal diversity associated with the intertidal forests of Southern China

Background

Mangroves are tropical and subtropical intertidal forests colonising sheltered coasts across the world. They host a unique faunal community, dominated by brachyuran crabs and gastropods. These invertebrates strongly contribute to the functionality of the entire forest. The reliable assessment of mangrove faunal diversity is, thus, a crucial step for efficient management and conservation plans, but it is hindered by difficulties in species identification. Here we provide a verified DNA barcode library for brachyuran crabs and gastropods inhabiting the mangroves of the Greater Bay Area, Southern China. In particular, we collected and morphologically identified 1100 specimens of mangrove associated brachyuran crabs and gastropods. The partial sequences of the mtDNA cytochrome oxidase subunit I gene were obtained from 275 specimens. Barcode sequences were then used to delineate Molecular Operational Taxonomic Units (MOTUs), employing three different delimitation methods: the automatic barcode gap discovery (ABGD) method, the general mixed Yule coalescent (GMYC) model and a Bayesian implementation of the Poisson tree processes (bPTP) model.

Results

By integrating DNA barcodes with morphology, we identified 44 gastropod species and 58 brachyuran species associated with Hong Kong mangroves, with five and seven new records, for gastropods and crabs, respectively, for the Greater Bay Area. The delineation of MOTUs based on barcode sequences revealed a strong congruence between morphological and molecular identification for both taxa, showing the high reliability of the barcode library.

Conclusions

This study provides the first reference barcode library for mangrove-associated macrobenthic fauna in the Greater Bay Area and represents a reliable tool to management and conservation plans. Our molecular analyses resolved long lasting taxonomic misidentifications and inconsistencies and updated the knowledge on the geographical distribution of Asian mangrove associated fauna, ultimately highlighting a level of biodiversity higher than previously thought for Southern China.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01914-6.

Conspicuous genetic similarity within a widely distributed and newly described species of Parasesarma De Man, 1895 from Western Pacific oceanic islands, with notes on the allied P. calypso group (Crustacea : Brachyura : Sesarmidae)

Some brachyuran crab species of the Western Pacific appear to be widespread throughout the region and distributed across a large geographic area, without obvious phylogeographic structuring. In the present study, we describe a new species of Parasesarma that appears to be restricted to Western Pacific islands (so far Guam, Palau, Vanuatu, Fiji, Wallis and New Caledonia). Comparisons of partial sequences of the COX1 gene show that individuals of this species, though from relatively isolated and widely separated islands, are monophyletic and, surprisingly, genetically uniform. These results give credence to the hypothesis that these oceanic islands serve as ‘stepping stones’ for the current-mediated dispersal and genetic homogenisation of coastal–littoral marine species. Morphologically, the new species differs most significantly from similar congeners in the tuberculation pattern of the chelar dactyli, whereas genetically it is markedly divergent from other morphologically similar species of Parasesarma, with a minimum COX1 p-distance of 6.9%. With such evidence, the new species is here formally described as Parasesarma daviei sp. nov. It is the fifth species of Parasesarma reported from oceanic islands of the Western Pacific. Compared to other congeners, P. daviei sp. nov. shows a close relationship with a clade including P. calypso. Therefore, P. calypso (De Man, 1895), and three of its former subspecies or varieties were subjected to a closer examination and are here rediagnosed and illustrated. In consequence, we suggest full species status for P. kuekenthali (De Man, 1902), P. lanchesteri (Tweedie, 1936), and P. ellenae (Pretzmann, 1968).

Taxonomic reassessment of Parasesarma (Crustacea: Brachyura: Decapoda: Sesarmidae) based on genetic and morphological comparisons, with the description of a new genus

Parasesarma is a species-rich genus whose representatives are common in wetlands and mangroves of the Indo-Pacific. Morphologically, the genus is heterogeneous and has been postulated to constitute a polyphyletic taxon. In the present study, most species of Parasesarma are re-evaluated phylogenetically, using mitochondrial and nuclear molecular markers. The results show that the majority of the examined species cluster consistently with the type species Parasesarma plicatum. However, some species, among them the tree-climbing Parasesarma leptosoma, are clearly separated from this main clade of Parasesarma, forming a second stable monophyletic group, distinct from other known genera. Based on these results, and with additional support by morphological diagnoses highlighting consistent differences between the two species groups, we propose a new genus for the species clustering around P. leptosoma, proposing the new name Leptarma gen. nov.

Revision of the Parasesarma guttatum species complex reveals a new pseudocryptic species in south-east African mangroves

Parasesarma De Man, 1895 is the most speciose genus in the family Sesarmidae (Decapoda: Brachyura: Thoracotremata). In the western Indian Ocean, Parasesarma is represented by five species only, although some genetic evidence suggests that P. guttatum could be a species complex comprising two cryptic species. Accordingly, P. guttatum is here split into two pseudocryptic species, and a new species, Parasesarma capensis, sp. nov., is described. P. capensis, sp. nov. fills the same ecological niche as P. guttatum south of the Mozambique Channel. While variation in mitochondrial DNA and morphological differences clearly distinguish the two species, there is no nuclear genetic variation. This may reflect a short history of reproductive isolation. The distinguishing morphological characters of the new species are the 13–15 rounded tubercles on the movable finger, the upper surface of the palm with three transverse crests (one regularly tuberculate and two pectinated), and the shape of the first gonopod. Phylogenetic inference analyses show a sister-species relationship between P. guttatum and P. capensis, sp. nov., and strongly suggest that at least two East African Parasesarma species need a taxonomic revision. The description of this new sesarmid species from the south-eastern African coast sheds new light on the overall biogeographic patterns and general biodiversity of this taxon within the western Indian Ocean.