Relating divergence in polychaete musculature to different burrowing behaviors: A study using opheliidae (Annelida)

A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea

Background

Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia.

New information

A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.

Why animals construct helical burrows: Construction vs. post-construction benefits

The extended phenotype of helical burrowing behavior in animals has evolved independently many times since the Cambrian explosion (~540 million years ago [MYA]). A number of hypotheses have been proposed to explain the evolution of helical burrowing in certain taxa, but no study has searched for a general explanation encompassing all taxa. We reviewed helical burrowing in both extant and extinct animals and from the trace fossil record and compiled 10 hypotheses for why animals construct helical burrows, including our own ideas. Of these, six are post-construction hypotheses-benefits to the creator or offspring, realized after burrow construction-and four are construction hypotheses reflecting direct benefits to the creator during construction. We examine the fit of these hypotheses to a total of 21 extant taxa and ichnotaxa representing 59-184 possible species. Only two hypotheses, antipredator and biomechanical advantage, cannot be rejected for any species (possible in 100% of taxa), but six of the hypotheses cannot be rejected for most species (possible in 86%-100% of taxa): microclimate buffer, reduced falling sediment (soil), anticrowding, and vertical patch. Four of these six are construction hypotheses, raising the possibility that helical burrowing may have evolved without providing post-construction benefits. Our analysis shows that increased drainage, deposit feeding, microbial farming, and offspring escape cannot explain helical burrowing behavior in the majority of taxa (5%-48%). Overall, the evidence does not support a general explanation for the evolution of helical burrowing in animals. The function and evolution of the helix as an extended phenotype seems to provide different advantages for different taxa in different environments under different physicochemical controls (some traces/tracemakers are discussed in more detail due to their association with body fossils and well-constrained physicochemical parameters). Although direct tests of many of the hypotheses would be difficult, we nevertheless offer ways to test some of the hypotheses for selected taxa.

Soft skeletons transmit force with variable gearing

A hydrostatic skeleton allows a soft body to transmit muscular force via internal pressure. A human's tongue, an octopus' arm and a nematode's body illustrate the pervasive presence of hydrostatic skeletons among animals, which has inspired the design of soft engineered actuators. However, there is a need for a theoretical basis for understanding how hydrostatic skeletons apply mechanical work. We therefore modeled the shape change and mechanics of natural and engineered hydrostatic skeletons to determine their mechanical advantage (MA) and displacement advantage (DA). These models apply to a variety of biological structures, but we explicitly consider the tube feet of a sea star and the body segments of an earthworm, and contrast them with a hydraulic press and a McKibben actuator. A helical winding of stiff, elastic fibers around these soft actuators plays a critical role in their mechanics by maintaining a cylindrical shape, distributing forces throughout the structure and storing elastic energy. In contrast to a single-joint lever system, soft hydrostats exhibit variable gearing with changes in MA generated by deformation in the skeleton. We found that this gearing is affected by the transmission efficiency of mechanical work (MA×DA) or, equivalently, the ratio of output to input work. The transmission efficiency changes with the capacity to store elastic energy within helically wrapped fibers or associated musculature. This modeling offers a conceptual basis for understanding the relationship between the morphology of hydrostatic skeletons and their mechanical performance.

New species of Pseudoscalibregma Ashworth, 1901 (Annelida: Scalibregmatidae Malmgren, 1867) from Brazil

Pseudoscalibregma Ashworth, 1901 is a small genus of the family Scalibregmatidae Malmgren, 1867. Currently, a total of eight valid species are accepted. Of these, the majority are found at great depths. This work contains the first report of Pseudoscalibregma to the Brazilian coast, with the description of three new species: Pseuscalibregma ermindae sp. nov., P. magalhaesi sp. nov. and P. parapari sp. nov. The material was sampled from the Brazilian southeast region, on Campos and Santos sedimentary basins, during scientific expeditions called Santos ProjectSantos Basin Environmental Characterization and Ambes ProjectEsprito Santo Basin Assessment Project, both coordinated by PETROBRAS/CENPES. We also include an identification key to Pseudoscalibregma species.

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

Background

The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.

Methods

The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.

Results and Discussion

mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.

Fundamentals of burrowing in soft animals and robots

Creating burrows through natural soils and sediments is a problem that evolution has solved numerous times, yet burrowing locomotion is challenging for biomimetic robots. As for every type of locomotion, forward thrust must overcome resistance forces. In burrowing, these forces will depend on the sediment mechanical properties that can vary with grain size and packing density, water saturation, organic matter and depth. The burrower typically cannot change these environmental properties, but can employ common strategies to move through a range of sediments. Here we propose four challenges for burrowers to solve. First, the burrower has to create space in a solid substrate, overcoming resistance by e.g., excavation, fracture, compression, or fluidization. Second, the burrower needs to locomote into the confined space. A compliant body helps fit into the possibly irregular space, but reaching the new space requires non-rigid kinematics such as longitudinal extension through peristalsis, unbending, or eversion. Third, to generate the required thrust to overcome resistance, the burrower needs to anchor within the burrow. Anchoring can be achieved through anisotropic friction or radial expansion, or both. Fourth, the burrower must sense and navigate to adapt the burrow shape to avoid or access different parts of the environment. Our hope is that by breaking the complexity of burrowing into these component challenges, engineers will be better able to learn from biology, since animal performance tends to exceed that of their robotic counterparts. Since body size strongly affects space creation, scaling may be a limiting factor for burrowing robotics, which are typically built at larger scales. Small robots are becoming increasingly feasible, and larger robots with non-biologically-inspired anteriors (or that traverse pre-existing tunnels) can benefit from a deeper understanding of the breadth of biological solutions in current literature and to be explored by continued research.

Redescription of a rarely encountered species Travisachinensis Grube, 1869 (Annelida, Travisiidae), including a description of a new species of Travisa from Amoy, China

The original description of Travisiachinensis Grube, 1869 was incomplete, leading to confusion with other species. To clarify the status of this species, we provide a redescription of, and remarks on, T.chinensis based on an examination of the type specimen. We also describe Travisiaamoyanus sp. nov., collected from Xiamen (Amoy), China, and originally identified as T.chinensis by Monro (1934). The new species can be distinguished from its congeners by a combination of the following characters: the total number of segments (34 or 35) and chaetigers (33 or 34), parapodial lappets first from chaetiger 15, and a pygidium with a large ventral triangular cirrus and about six encircling lateral cirri. Genetic distances and phylogenetic analyses based on the mitochondrial (16S rRNA) and nuclear (18S rRNA) genes support the identity of the new species.

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.

On the Systematics and Biodiversity of the Opheliidae and Scalibregmatidae

In this paper we review the systematics, diversity, and ecology of two related annelid families: Opheliidae Malmgren, 1867 and Scalibregmatidae Malmgren, 1867. Opheliids are deposit-feeders and that are mainly found as burrowers in sandy sediments. Morphologically, opheliids are characterized by the smooth cuticle, as well as the presence of a conspicuous ventral groove, reduced parapodia, and a tubular-shaped structure often projecting from the posterior end. Scalibregmatids are also deposit-feeders, but compared to opheliids, they have a characteristic arenicoliform body, a T-shaped anterior end and a glandular, reticulated epidermis. For each family, we summarize the available information about the evolutionary relationships, taxonomic history, geographical distribution, ecological preferences and diversity of life strategies along with the techniques most commonly used for their study. By highlighting the main gaps in knowledge on each of these topics, this review ultimately aims at stimulating further research into members of these two families in the future.

The 20-million-year old lair of an ambush-predatory worm preserved in northeast Taiwan

The feeding behavior of the giant ambush-predator "Bobbit worm" (Eunice aphroditois) is spectacular. They hide in their burrows until they explode upwards grabbing unsuspecting prey with a snap of their powerful jaws. The still living prey are then pulled into the sediment for consumption. Although predatory polychaetes have existed since the early Paleozoic, their bodies comprise mainly soft tissue, resulting in a very incomplete fossil record, and virtually nothing is known about their burrows and behavior beneath the seafloor. Here we use morphological, sedimentological, and geochemical data from Miocene strata in northeast Taiwan to erect a new ichnogenus, Pennichnus. This trace fossil consists of an up to 2 m long, 2-3 cm in diameter, L-shaped burrow with distinct feather-like structures around the upper shaft. A comparison of Pennichnus to biological analogs strongly suggests that this new ichnogenus is associated with ambush-predatory worms that lived about 20 million years ago.

Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Annelida: Capitellidae, Opheliidae, Scalibregmatidae, and Travisiidae

We present DNA taxonomy of abyssal polychaete worms from the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruises ‘AB01’ and ‘AB02’ to the UK Seabed Resources Ltd (UKSRL) polymetallic nodule exploration contract area ‘UK-1’, the Ocean Mineral Singapore exploration contract area ‘OMS-1’ and an Area of Particular Environmental Interest, ‘APEI-6’. This is the fourth paper in a series to provide regional taxonomic data with previous papers reporting on Cnidaria, Echinodermata and Mollusca. Taxonomic data are presented for 23 species from 85 records within four polychaete families: Capitellidae, Opheliidae, Scalibregmatidae and Travisiidae, identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. Two taxa (genetically separated from one another) morphologically matched the same known cosmopolitan species, Ophelinaabranchiata that has a type locality in a different ocean basin and depth from where no genetic data was available. These two species were assigned the open nomenclature ‘cf.’ as a precautionary approach in taxon assignments to avoid over-estimating species ranges. Twelve (12) taxa are here described as new species, Ammotrypanellakeenanisp. nov., Ammotrypanellakerstenisp. nov., Ophelinacurlisp. nov., Ophelinaganaesp. nov., Ophelinajuhazisp. nov., Ophelinamartinezarbizuisp. nov., Ophelinameyeraesp. nov., Ophelinanunnallyisp. nov., Oligobregmabrasieraesp. nov., Oligobregmatanisp. nov., Oligobregmawhaleyisp. nov. and Travisiaziegleraesp. nov. For the remaining nine taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The CCZ is a region undergoing intense exploration for potential deep-sea mineral extraction from polymetallic nodules. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.

Kinematics of burrowing by peristalsis in granular sands

Peristaltic burrowing in muds applies normal forces to burrow walls, which extend by fracture, but the kinematics and mechanics of peristaltic burrowing in sands has not been explored. The opheliid polychaete, Thoracophelia mucronata, uses direct peristalsis to burrow in beach sands, using kinematics consistent with the “dual anchor system” of burrowing used by diverse organisms. In addition to expansions associated with a constrictive direct peristaltic wave, worms alternately expand the head region, which is separated by septa from the open body cavity, and expansible lateral ridges that protrude from the 10th setiger. Tracking of fluorescent-dyed chaetae showed that the body wall advances while segments are thin, then stationary segments expand, applying normal forces to burrow walls. These normal forces likely compact burrow walls and serve as anchors. Perhaps more importantly, peristaltic movements minimize friction with the burrow wall, which would expand dilatant sands. Considerable slipping of worms burrowing in a lower-density sand analog suggests that this dual-anchor peristaltic burrowing may be limited to a narrow range of mechanical properties of substrata, consistent with the limited habitat of T. mucronata in a narrow swash zone on dissipative beaches.

Burrowing by small polychaetes - mechanics, behavior and muscle structure of Capitella sp

Worms of different sizes extend burrows through muddy sediments by fracture, applying dorso-ventral forces that are amplified at the crack tip. Smaller worms displace sediments less than larger worms and therefore are limited in how much force they can apply to burrow walls. We hypothesized that small worms would exhibit a transition in burrowing mechanics, specifically a lower limit in body size for the ability to burrow by fracture, corresponding with an ontogenetic transition in muscle morphology. Kinematics of burrowing in a mud analog, external morphology and muscle arrangement were examined in juveniles and adults of the small polychaete Capitella sp. We found that it moves by peristalsis, and no obvious differences were observed among worms of different sizes; even very small juveniles were able to burrow through a clear mud analog by fracture. Interestingly, we found that in addition to longitudinal and circular muscles needed for peristaltic movements, left- and right-handed helical muscles wrap around the thorax of worms of all sizes. We suggest that in small worms helical muscles may function to supplement forces generated by longitudinal muscles and to maintain hydrostatic pressure, enabling higher forces to be exerted on the crack wall. Further research is needed, however, to determine whether surficial sediments inhabited by small worms fail by fracture or plastically deform under forces of the magnitudes applied by Capitella sp.