Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Complete Mitochondrial Genomes and Phylogenetic Analysis of Genus Henricia (Asteroidea: Spinulosida: Echinasteridae)

The genus Henricia is known to have intraspecific morphological variations, making species identification difficult. Therefore, molecular phylogeny analysis based on genetic characteristics is valuable for species identification. We present complete mitochondrial genomic sequences of Henricia longispina aleutica, H. reniossa, and H. sanguinolenta for the first time in this study. This study will make a significant contribution to our understanding of Henricia species and its relationships within the class Asteroidea. Lengths of mitochondrial genomes of the three species are 16,217, 16,223, and 16,194 bp, respectively, with a circular form. These genomes contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a D-loop. The gene order and direction aligned with other asteroid species. Phylogenetic relationship analysis showed that our Henricia species were in a monophyletic clade with other Henricia species and in a large clade with species (Echinaster brasiliensis) from the same family. These findings provide valuable insight into understanding the phylogenetic relationships of species in the genus Henricia.

The complete mitochondrial genome of Poraniopsis inflata (Asteroidea: Valvatida: Poraniidae) from Dokdo Island, Korea

This study presents the complete mitochondrial genome sequence of Poraniopsis inflata, providing valuable information on its genetic and taxonomic studies. Through next-generation sequencing, we successfully obtained the complete mitogenome of P. inflata, spanning a length of 16,322 bp. This genome structure encompasses 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The phylogenetic analysis, based on a dataset of 13 PCG sequences, illuminated the phylogenetic relationships of P. inflata with other species of class Asteroidea and a species of echinoderm classes. The maximum likelihood phylogenetic tree showed that P. inflata closely clustered with Linckia laevigata. By revealing its mitochondrial genome and positioning it within the Asteroidea lineage, this study provides insights into the phylogenetic context of P. inflata.

A 104-Ma record of deep-sea Atelostomata (Holasterioda, Spatangoida, irregular echinoids) - a story of persistence, food availability and a big bang

Deep-sea macrobenthic body fossils are scarce due to the lack of deep-sea sedimentary archives in onshore settings. Therefore, hypothesized migrations of shallow shelf taxa into the deep-sea after phases of mass extinction (onshore-offshore pattern in the literature) due to anoxic events is not constrained by the fossil record. To resolve this conundrum, we investigated 1,475 deep-sea sediment samples from the Atlantic, Pacific and Southern oceans (water depth ranging from 200 to 4,700 m), providing 41,460 spine fragments of the crown group Atelostomata (Holasteroida, Spatangoida). We show that the scarce fossil record of deep-sea echinoids is in fact a methodological artefact because it is limited by the almost exclusive use of onshore fossil archives. Our data advocate for a continuous record of deep-sea Atelostomata back to at least 104 Ma (late early Cretaceous), and literature records suggest even an older age (115 Ma). A gradual increase of different spine tip morphologies from the Albian to the Maastrichtian is observed. A subsequent, abrupt reduction in spine size and the loss of morphological inventory in the lowermost Paleogene is interpreted to be an expression of the "Lilliput Effect", related to nourishment depletion on the sea floor in the course of the Cretaceous-Paleogene (K-Pg) Boundary Event. The recovery from this event lasted at least 5 Ma, and post-K-Pg Boundary Event assemblages progress-without any further morphological breaks-towards the assemblages observed in modern deep-sea environments. Because atelostomate spine morphology is often species-specific, the variations in spine tip morphology trough time would indicate species changes taking place in the deep-sea. This observation is, therefore, interpreted to result from in-situ evolution in the deep-sea and not from onshore-offshore migrations. The calculation of the "atelostomate spine accumulation rate" (ASAR) reveals low values in pre-Campanian times, possibly related to high remineralization rates of organic matter in the water column in the course of the mid-Cretaceous Thermal Maximum and its aftermath. A Maastrichtian cooling pulse marks the irreversible onset of fluctuating but generally higher atelostomate biomass that continues throughout the Cenozoic.

Strategy of micro-environmental adaptation to cold seep among different brittle stars’ colonization

Diffusing fluid from methane seepage in cold seep field creates zones with physicochemical gradients and divergent ecosystems like the mussel beds and clam beds. Three species of brittle stars (Ophiuroidea) were discovered in the Haima cold seep fields, of which Ophiophthalmus serratus and Histampica haimaensis were found on top of or within mussel beds and clam beds, whereas Amphiura sp. was only collected from muds in the clam bed assemblage. Here, we evaluated the genetic signatures of micro-environmental adaptation of brittle stars to cold seep through the comparison of mitogenomes. This study provided two complete mitogenome sequences of O. serratus and Amphiura sp. and compared with those of H. haimaensis and other non-seep species. We found that the split events of the seep and non-seep species were as ancient as the Cretaceous period (∼148–98 Mya). O. serratus and H. haimaensis display rapid residue mutation and mitogenome rearrangements compared to their shallow or deep-sea relatives, in contrast, Amphiura sp. only show medium, regardless of nucleotide mutation rate or mitogenome rearrangement, which may correlate with their adaptation to one or two micro-ecosystems. Furthermore, we identified 10 positively selected residues in ND4 in the Amphiura sp. lineage, suggesting important roles of the dehydrogenase complex in Amphiura sp. adaptive to the cold seep environment. Our results shed light on the different evolutionary strategies during colonization in different micro-environments.

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser ^AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser ^AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.