Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurus inferred from multiple mitochondrial genes, with special emphasis on the evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus

Abstract

The hermit crab genus Pagurus exhibits high species diversity and a wide geological distribution. Despite the high species diversity of hermit crabs in the western Pacific coast of Japan, molecular phylogenetic studies of these species have yet to be conducted. To investigate their molecular phylogeny and genetic diversity, we obtained nearly complete mitochondrial genome sequences for ten Pagurus species found along the Pacific coast of Japan by next-generation sequencing, which were compared to other congeners deposited in the GenBank database. The genomes ranged from 13,458 to 16,401 base pairs in length, possessing 13 protein-coding genes, 2 rRNAs, and 22 tRNA genes. Based on the reconstructed phylogeny, we found that (1) Japanese Pagurus species separated into three groups, nested within the Northern Pacific species. (2) Pagurus lanuginosus and Pagurus maculosus, showed high morphological similarities, implying close kinship. Indeed, these two species were genetically closest to each other, compared to the remaining species studied. (3) An unspecified specimen sampled from the deep sea, which morphologically resembled Pagurus, might be a member of the Pagurus genus, but is genetically distant from the other Japanese Pagurus species. The novel data reported here may provide new perspectives for systematic studies of hermit crabs; these results provide important information that will facilitate population-level research and identifying intraspecific variation of these non-model, but ecologically important, decapod species.

Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura

“…For example, abundant gene rearrangement is evident in sea cucumber [ 10], cephalopod [ 11], mollusk [ 12], insect [ 13], and crabs [ 4]. Although a gradually growing number of gene rearrangement in hermit crabs (Paguridae) has been discovered [ 2, [14][15][16], it is surprising that gene rearrangement in its close relatives, the terrestrial hermit crab (Coenobitidae), was overlooked until 2018. It was found that large-scale gene rearrangements existed in the mitogenome of terrestrial hermit crabs, differing from that of the reported crabs [ 5].…”

Complete mitochondrial genome of the intertidal hermit crab, Pagurus similis (Crustacea, Anomura)

“…The complete mitogenome of P. similis was 15,683 bp in length and contained the typical set of 13 PCGs, 22 tRNAs, 2 rRNAs, and an AT-rich region. Overall, gene order and content of P. similis mitogenome were identical to those of Paguridae species (Hickerson and Cunningham 2000;Sultana et al 2018;Gong et al 2019). The nucleotide composition of P. similis mitogenome is heavily biased toward A þ T nucleotides, accounting for 36% A, 16% C, 11% G, and 37% T. In particular, the highly A þ T biased value (71.4%) was slightly higher than the value of P. nigrofascia mitogenome (Gong et al 2019), as mainly differs in the AT-rich region.…”

“…Since high-level taxonomic characterization of the genus Pagurus is complex due to morphologically heterogeneous characteristics and uncertain registration of many new species to this genus (Olgu ın and Mantelatto 2013), accumulation of the genomic information of Paguridae species is strongly needed to clarify their molecular phylogeny and genetic diversity (Bracken-Grissom et al 2013). Despite the high species diversity and abundance of the genus Pagurus, only a few reports have been suggested on genomic characteristics and organization of whole mitogenomes in Paguridae species and studies on indepth molecular phylogenetic relationship have yet to be conducted (Hickerson and Cunningham 2000;Sultana et al 2018;Gong et al 2019). Of genus Pagurus, whole mitochondrial genome information was firstly applied on P. longicarpus to understand genetic variation and unique gene rearrangements (Hickerson and Cunningham 2000).…”

“…Of genus Pagurus, whole mitochondrial genome information was firstly applied on P. longicarpus to understand genetic variation and unique gene rearrangements (Hickerson and Cunningham 2000). A wide range of genetic diversity of the genus Pagurus and their phylogenetic relationships was suggested using nearly complete mitochondrial genome sequences for 10 Pagurus species (Sultana et al 2018). Recently, large-scale gene rearrangements were reported in the P. nigrofascia mitogenome and the phylogenetic relationship was suggested in the Anomura (Gong et al 2019).…”

Taxonomy and molecular phylogeny analysis of the genus Diogenes “Edwardsii group” (Decapoda: Anomora: Diogenidae) based on mitochondrial DNA sequences

“…DNA barcoding is a useful tool for the taxonomic classification and identification of species by sequencing a very short, standardized DNA sequence in a well-defined gene (Purty and Chatterjee 2016;Madduppa et al 2017;Landschoff and Gouws 2018). The mitochondrial DNA is widely used in identifying a species from Indonesia marine invertebrates (Aprilia et al 2014;Kurniasari et al 2014;Sahriyani et al 2014;Toha et al 2015;Saleky et al 2016;Madduppa et al 2016;Dailami et al 2018;Pranata et al 2020;Hikam et al 2021), discover new species in a wide range of taxa (Wang et al 2017), and used for phylogenetic studies (Galan et al 2018;Sultana et al 2018;Mantelatto et al 2021). DNA barcoding has advantages in precision and accuracy in the safe identification of species compared with the morphological observations (Madduppa et al 2017;Fuentes-López et al 2020).…”