-
Scientific Reports Sep 2021Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular...
Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular era is a complicated task that has many pitfalls. In the present study we use particular examples of common but difficult to distinguish European species within the genus of Polycera (Nudibranchia, Mollusca) to discuss the general issues of the "cryptic species" problem that has broad biological and interdisciplinary importance and can significantly impede ecological, evolutionary, and other biodiversity-related research. The largest dataset of molecular and morphological information for European nudibranchs ever applied encompasses a wide geographical area and shapes a robust framework in this study. Four species are recognized in the species complex, including a new one. It is shown that a lack of appropriate taxonomic analysis led recently to considerable errors in species identity assessment of this complex. Chromatic polymorphism for each species is mapped in a periodic-like framework and combined with statistical analysis of the diagnostic features that considerably facilitates identification of particular species in the complex for biologists and practitioners. The present study evidently shows that "cryptic" and "non-cryptic" components are present within the same species. Therefore, this species complex is well suited for the exploring and testing of general biological problems. One of the main conclusions of this study is that division of biological diversity into "cryptic" and "non-cryptic" components is counterproductive. We propose that the central biological phenomenon of a species can instead be universally designated as multilevel organismal diversity thereby provide a practical set of methods for its investigation.
Topics: Animals; Biodiversity; Biological Evolution; Europe; Gastropoda; Genes, Mitochondrial; Genetic Variation; Phenotype; Phylogeny; Phylogeography; Terminology as Topic
PubMed: 34526521
DOI: 10.1038/s41598-021-94863-5 -
PloS One 2021The antiquity and nature of coastal resource procurement is central to understanding human evolution and adaptations to complex environments. It has become increasingly...
The antiquity and nature of coastal resource procurement is central to understanding human evolution and adaptations to complex environments. It has become increasingly apparent in global archaeological studies that the timing, characteristics, and trajectories of coastal resource use are highly variable. Within Africa, discussions of these issues have largely been based on the archaeological record from the south and northeast of the continent, with little evidence from eastern coastal areas leaving significant spatial and temporal gaps in our knowledge. Here, we present data from Panga ya Saidi, a limestone cave complex located 15 km from the modern Kenyan coast, which represents the first long-term sequence of coastal engagement from eastern Africa. Rather than attempting to distinguish between coastal resource use and coastal adaptations, we focus on coastal engagement as a means of characterising human relationships with marine environments and resources from this inland location. We use aquatic mollusc data spanning the past 67,000 years to document shifts in the acquisition, transportation, and discard of these materials, to better understand long-term trends in coastal engagement. Our results show pulses of coastal engagement beginning with low-intensity symbolism, and culminating in the consistent low-level transport of marine and freshwater food resources, emphasising a diverse relationship through time. Panga ya Saidi has the oldest stratified evidence of marine engagement in eastern Africa, and is the only site in Africa which documents coastal resources from the Late Pleistocene through the Holocene, highlighting the potential archaeological importance of peri-coastal sites to debates about marine resource relationships.
Topics: Adaptation, Physiological; Africa, Eastern; Animals; Archaeology; Caves; Humans; Kenya; Mollusca; Shellfish
PubMed: 34437643
DOI: 10.1371/journal.pone.0256761 -
PeerJ 2022The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been...
The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda .), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.
Topics: Animals; Gastropoda; Phylogeny; Mollusca; Genome; Transcriptome
PubMed: 35497189
DOI: 10.7717/peerj.13285 -
RNA Biology Nov 2021Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of...
Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
Topics: Animals; Gene Expression Regulation; Genome; Genome-Wide Association Study; MicroRNAs; Mollusca
PubMed: 33356816
DOI: 10.1080/15476286.2020.1867798 -
International Journal of Molecular... Jun 2021In the mid-1950s, Bert Lester Vallee and his colleague Marvin Margoshes discovered a molecule referred to today as metallothionein (MT). Meanwhile, MTs have been shown...
In the mid-1950s, Bert Lester Vallee and his colleague Marvin Margoshes discovered a molecule referred to today as metallothionein (MT). Meanwhile, MTs have been shown to be common in many biological organisms. Despite their prevalence, however, it remains unclear to date what exactly MTs do and how they contribute to the biological function of an organism or organ. We investigate why biochemical research has not yet been able to pinpoint the function(s) of MTs. We shall systematically examine both the discovery of and recent research on Dr. Vallee's beloved family of MT proteins utilizing tools from philosophy of science. Our analysis highlights that Vallee's initial work exhibited features prototypical of a developing research tradition: it was upward-looking, exploratory, and utilized mere interactions. Since the 1960s, MT research has increasingly become intervention- and hypothesis-based while it remained largely upward-looking in character. Whilst there is no reason to think that upward-looking research cannot successfully yield structure-function mappings, it has not yet been successful in the case of MTs. Thus, we suggest it might be time to change track and consider other research strategies looking into the evolution of MTs. Recent studies in mollusks render research in this direction worthy of pursuit.
Topics: Animals; Metallothionein; Mollusca; Structure-Activity Relationship
PubMed: 34206018
DOI: 10.3390/ijms22115984 -
The Journal of Experimental Biology Jan 2011Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into...
Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO(2) fixation (photosynthesis). 'Solar-powered' sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a 'plant' when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ~10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating 'green animal' provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.
Topics: Animals; Biological Evolution; Chlorophyta; Gene Expression Profiling; Gene Transfer, Horizontal; Mollusca; Photosynthesis; Plastids; Symbiosis
PubMed: 21177950
DOI: 10.1242/jeb.046540 -
Scientific Reports Mar 2019Cambrian annelids are strikingly diverse and reveal important details of annelid character acquisition. Their contribution, however, to a wider understanding of the...
Cambrian annelids are strikingly diverse and reveal important details of annelid character acquisition. Their contribution, however, to a wider understanding of the evolution of the trochozoans (encompassing the annelids as well as such groups as the brachiopods and molluscs) remains limited. Thus the early annelids had been linked to a variety of cataphract Cambrian metazoans, notably Wiwaxia and the halkieriids, but recent work assigns such fossils to stem-group molluscs. Here we report two new annelids from the Lower Cambrian Chengjiang Lagerstätte, South China. Ipoliknus avitus n. gen., n. sp. is biramous with neurochaetae and notochaetae, but significantly also bears dorsal spinose sclerites and dorso-lateral dentate sclerites. Adelochaeta sinensis n. gen., n. sp. is unique amongst Cambrian polychaetes in possessing the rod-like supports of the parapodia known as aciculae. This supports phylogenetic placement of Adelochaeta as sister to some more derived aciculate Palaeozoic taxa, but in contrast Ipoliknus is recovered as the most basal of the stem-group annelids. Sclerites and chaetae of I. avitus are interpreted respectively as the remnants and derivatives of a once more extensive cataphract covering that was a characteristic of more primitive trochozoans. The two sets of chaetae (noto- and neurochaetae) and two sets of sclerites (spinose and dentate) suggest that in a pre-annelid an earlier and more complete scleritome may have consisted of four zones of sclerites. Other cataphract taxa from the Lower Palaeozoic show a variety of scleritome configurations but establishing direct links with such basal annelids as Ipoliknus at present must remain conjectural.
Topics: Animals; Annelida; Biological Evolution; China; Fossils; Mollusca; Phylogeny
PubMed: 30894583
DOI: 10.1038/s41598-019-40841-x -
PloS One 2023Hemocyanins are multimeric oxygen transport proteins present in the blood of arthropods and molluscs, containing up to 8 oxygen-binding functional units per monomer. In...
Hemocyanins are multimeric oxygen transport proteins present in the blood of arthropods and molluscs, containing up to 8 oxygen-binding functional units per monomer. In molluscs, hemocyanins are assembled in decamer 'building blocks' formed of 5 dimer 'plates', routinely forming didecamer or higher-order assemblies with d5 or c5 symmetry. Here we describe the cryoEM structures of the didecamer (20-mer) and tridecamer (30-mer) forms of a novel hemocyanin from the slipper limpet Crepidula fornicata (SLH) at 7.0 and 4.7 Å resolution respectively. We show that two decamers assemble in a 'tail-tail' configuration, forming a partially capped cylinder, with an additional decamer adding on in 'head-tail' configuration to make the tridecamer. Analysis of SLH samples shows substantial heterogeneity, suggesting the presence of many higher-order multimers including tetra- and pentadecamers, formed by successive addition of decamers in head-tail configuration. Retrieval of sequence data for a full-length isoform of SLH enabled the use of Alphafold to produce a molecular model of SLH, which indicated the formation of dimer slabs with high similarity to those found in keyhole limpet hemocyanin. The fit of the molecular model to the cryoEM density was excellent, showing an overall structure where the final two functional units of the subunit (FU-g and FU-h) form the partial cap at one end of the decamer, and permitting analysis of the subunit interfaces governing the assembly of tail-tail and head-tail decamer interactions as well as potential sites for N-glycosylation. Our work contributes to the understanding of higher-order oligomer formation in molluscan hemocyanins and demonstrates the utility of Alphafold for building accurate structural models of large oligomeric proteins.
Topics: Animals; Hemocyanins; Cryoelectron Microscopy; Mollusca; Models, Molecular; Arthropods; Gastropoda; Polymers
PubMed: 37347755
DOI: 10.1371/journal.pone.0287294 -
BMC Biology Feb 2018The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation...
BACKGROUND
The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed.
RESULTS
We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria). We demonstrated that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with deionized water was sufficient for karyotyping; growing cells in culture was not necessary. The obtained karyotypes allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla this protocol could be effectively coupled with downstream applications, such as chromosome fluorescent in situ hybridization.
CONCLUSIONS
Our simple and inexpensive chromosome preparation protocol can be readily adapted to new invertebrate research organisms to accelerate the discovery of novel genomic patterns across the branches of the tree of life.
Topics: Animals; Chromosomes; Embryo, Nonmammalian; Invertebrates; Karyotyping; Mollusca; Planarians; Platyhelminths; Sea Anemones; Snails
PubMed: 29482548
DOI: 10.1186/s12915-018-0497-4 -
Scientific Reports Nov 2022Dorid nudibranchs are a large group of mollusks with approximately 2,000 recorded species. Although agreement exists on the monophyletic nature of the dorid nudibranch...
Dorid nudibranchs are a large group of mollusks with approximately 2,000 recorded species. Although agreement exists on the monophyletic nature of the dorid nudibranch group, the interfamily relationships of the suborder are subject to debate. Despite efforts to elucidate this issue using short molecular markers, the conclusiveness of the findings has been hindered by branching polytomy. Mitogenomes are known to be effective markers for use in phylogenetic investigations. In this study, eight mitogenomes of dorid nudibranchs were decoded and analyzed. Gene content and structure showed little change among species, reflecting the conserved mitogenomes of dorid nudibranchs. For most genes, the direction was typical for nudibranchs; nevertheless, tRNA had an inverse direction in Cadlinidae species. Phylogenetic trees based on nucleotide and amino acid datasets revealed a relatively consistent pattern of interfamily relationships with little difference for positions of Phyllidiidae and Cadlinidae. Species of Cadlinidae were clustered together and did not form a clade with Chromododidae. Additionally, Goniodorididae was sister to Aegiridae, whereas Discodoridae was sister to Dorididae. This finding was supported by tree topology test based on mitogenome data. The results of the present study indicate that complete mitogenomes are promising markers for investigating interfamily relationships among dorid nudibranchs.
Topics: Animals; Genome, Mitochondrial; Phylogeny; Gastropoda; RNA, Transfer; Mollusca
PubMed: 36335153
DOI: 10.1038/s41598-022-23400-9