Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods

Geometric morphometrics casts light on phylogenetic relevance of cephalopod beak morphological

The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.

SNP data reveals the complex and diverse evolutionary history of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) in the Asia-Pacific

The blue-ringed octopus species complex (Hapalochlaena spp.), known to occur from Southern Australia to Japan, currently contains four formally described species (Hapalochlaena maculosa, Hapalochlaena fasciata, Hapalochlaena lunulata and Hapalochlaena nierstraszi). These species are distinguished based on morphological characters (iridescent blue rings and/or lines) along with reproductive strategies. However, the observation of greater morphological diversity than previously captured by the current taxonomic framework indicates that a revision is required. To examine species boundaries within the genus we used mitochondrial (12S rRNA, 16S rRNA, cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII] and cytochrome b [Cytb]) and genome-wide SNP data (DaRT seq) from specimens collected across its geographic range including variations in depth from 3m to >100m. This investigation indicates substantially greater species diversity present within the genus Hapalochlaena than is currently described. We identified 10,346 SNPs across all locations, which when analysed support a minimum of 11 distinct clades. Bayesian phylogenetic analysis of the mitochondrial COI gene on a more limited sample set dates the diversification of the genus to ∼30mya and corroborates eight of the lineages indicated by the SNP analyses. Furthermore, we demonstrate that the diagnostic lined patterning of H. fasciata found in North Pacific waters and NSW, Australia is polyphyletic and therefore likely the result of convergent evolution. Several "deep water" (> 100m) lineages were also identified in this study with genetic convergence likely to be driven by external selective pressures. Examination of morphological traits, currently being undertaken in a parallel morphological study, is required to describe additional species within the complex.

Testing the systematic status of Homalictus and Rostrohalictus with weakened cross-vein groups within Halictini (Hymenoptera: Halictidae) using low-coverage whole-genome sequencing

The halictid genus Lasioglossum, as one of the most species-rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus, whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l. based on thousands of single-copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low-coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent-based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum. Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus. Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus. Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.

Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species

Genus Pinus is a widely dispersed genus of conifer plants in the Northern Hemisphere. However, the inadequate accessibility of genomic knowledge limits our understanding of molecular phylogeny and evolution of Pinus species. In this study, the evolutionary features of complete plastid genome and the phylogeny of the Pinus genus were studied. A total of thirteen divergent hotspot regions (trnk-UUU, matK, trnQ-UUG, atpF, atpH, rpoC1, rpoC2, rpoB, ycf2, ycf1, trnD-GUC, trnY-GUA, and trnH-GUG) were identified that would be utilized as possible genetic markers for determination of phylogeny and population genetics analysis of Pinus species. Furthermore, seven genes (petD, psaI, psaM, matK, rps18, ycf1, and ycf2) with positive selection site in Pinus species were identified. Based on the whole genome this phylogenetic study showed that twenty-four Pinus species form a significant genealogical clade. Divergence time showed that the Pinus species originated about 100 million years ago (MYA) (95% HPD, 101.76.35–109.79 MYA), in lateral stages of Cretaceous. Moreover, two of the subgenera are consequently originated in 85.05 MYA (95% HPD, 81.04–88.02 MYA). This study provides a phylogenetic relationship and a chronological framework for the future study of the molecular evolution of the Pinus species.

Sucker formation in a bigfin reef squid: Comparison between arms and tentacles

Cephalopods have acquired numerous novelties and expanded their habitats to various marine environments as highly agile predators. Among cephalopod novelties, multiple arms are used for complex behaviors, including prey capture. Suckers on arms are innovative features for realizing these arm functions. In addition, tentacles in Decapodiformes (squids and cuttlefishes) are arms specialized in prey capture and tentacular suckers show unique morphologies. However, little is known about the developmental process of sucker formation that should differ between tentacles and other arms. In this study, therefore, sucker formation processes on second arms and tentacles were observed and compared in a bigfin reef squid, Sepioteuthis lessoniana, to reveal the developmental processes forming the unique sucker morphologies, especially in tentacles. Morphological and histological observations of suckers during embryogenesis showed that, in second arms, the sucker-producing area appeared at the most distal part. At the most proximal side of the sucker-producing area, new sucker buds were isolated by invagination of the epithelial tissue. At the proximal arm parts, suckers with functional structures were observed. In tentacles, although the basic sucker formation pattern was similar to that in second arms, sucker formation started at earlier embryonic stages and the number of suckers was drastically increased compared to that in second arms. In addition, although four sucker rows were observed at the tentacular club, that is, the thickest part of a tentacle, our observations suggested that two sets of two sucker rows are compressed to form the four rows. Therefore, the sucker-formation processes are temporally and spatially different between arms and tentacles. In addition, S. lessoniana shows conserved and unique patterns of sucker formation in comparison with previously described species, suggesting that sucker formation patterns were diversified among Decapodiformes lineages.

Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns

Coleoids are the most diverse group of cephalopod mollusks. While their origin is date during the Mesozoic, the diversification pattern is unknown. However, two hypotheses have been proposed. The first suggests an increasing diversification rate after the Cretaceous-Paleogene extinction event (K-Pg) as consequence of empty habitats left by the ammonites and belemnites. The second hypothesis proposes a mid-Cenozoic increase in diversification rate related to distributional changes during ice ages and biotic interactions. To test these hypotheses, we estimated a lineage through time (LTT) and the gamma-statistic along with model-based diversification rates. These analyses were conducted on a dated molecular phylogeny for coleoids that we reconstructed using five molecular markers (cytochrome b, 16S rRNA, cytochrome oxidase I, rhodopsin, and PAX-6). Our divergence time estimation suggests that coleoids originated in the Mesozoic Era (Middle Triassic) and that both main clades (Decapodiformes and Octopodiformes) diverged in the Cretaceous/Jurassic Period. The LTT, gamma statistic, and diversification rates inferred with the Bayesian Analysis of Macro-evolutionary Mixtures (BAMM), indicate an acceleration in diversification rate over time since the origin of coleoids. Additionally, BAMM allowed us to detect abrupt increases in diversification rate before and after the K-Pg boundary. Our results partially support both hypotheses as all analyses indicate that the coleoid diversification rate was increasing during the Cenozoic. However, our results also indicate increasing diversification rates before the K-Pg boundary. We propose that the radiation of coleoids has been shaped by an acceleration in diversification rate over time, including exceptional episodes of abrupt increases before and after the K-Pg boundary.

A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Oceanic squids of the order Oegopsida are ecologically and economically important members of the pelagic environment. They are the most diverse group of cephalopods, with 24 families that are divergent morphologically. Despite their importance, knowledge of phylogenetic relationships among oegopsids is less than that among neritic cephalopods. Here, we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes for 35 selected oceanic squids, which were generated using genome skimming. We performed maximum likelihood and Bayesian inference analyses that included 21 of the 24 oegopsid families. In our analyses, the architeuthid, chiroteuthid and enoploteuthid family groups, which have been proposed previously based on morphological and natural history characteristics, were retrieved as monophyletic. The morphologically divergent Cranchiidae formed a well-supported clade with families Ommastrephidae and Thysanoteuthidae, with a unique mitochondrial gene order. The family Lycoteuthidae was revealed as paraphyletic and contained Pyroteuthidae. Thus, the two lycoteuthid subfamilies are herein elevated to family level, increasing the number of oegopsid squid families to 25. In order to describe the diversity and evolutionary trends of oegopsid squids accurately, the superfamilies Architeuthoidea, Chiroteuthoidea, Cranchioidea and Enoploteuthoidea are resurrected from the literature, and the superfamilies Cycloteuthoidea, Octopoteuthoidea and Pholidoteuthoidea are proposed. The phylogenetic positions of Gonatidae, Histioteuthidae and Onychoteuthidae were not stable in our phylogenetic analyses and are not assigned to a superfamily. This study supports the utility of genome skimming to solve the phylogenetic relationships of oceanic squids.

Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)

Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.

Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods

Phylogenetic relationships among the squids and cuttlefishes (Cephalopoda:Decapodiformes) have resisted clarification for decades, despite multiple analyses of morphological, molecular and combined data sets. More recently, analyses of complete mitochondrial genomes and hundreds of nuclear loci have yielded similarly ambiguous results. In this study, we re-evaluate hypotheses of decapodiform relationships by increasing taxonomic breadth and utilizing higher-quality genome and transcriptome data for several taxa. We also employ analytical approaches to (1) identify contamination in transcriptome data, (2) better assess model adequacy, and (3) account for potential biases. Using this larger data set, we consistently recover a clade comprising Myopsida (closed-eye squid), Sepiida (cuttlefishes), and Oegopsida (open-eye squid) that is sister to a Sepiolida (bobtail and bottletail squid) clade. Idiosepiida (pygmy squid) is consistently recovered as the sister group to all sampled decapodiform lineages. Further, a weighted Shimodaira-Hasegawa test applied to one of our larger data matrices rejects all alternatives to these ordinal-level relationships. At present, available nuclear genome-scale data support nested clades of relatively large-bodied decapodiform cephalopods to the exclusion of pygmy squids, but improved taxon sampling and additional genomic data will be needed to test these novel hypotheses rigorously.

Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

BACKGROUND

Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland.

FINDINGS

To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non-tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source.

CONCLUSIONS

We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.

A polyvalent and universal tool for genomic studies in gastropod molluscs (Heterobranchia)

Molluscs are the second most diverse animal phylum and heterobranch gastropods present ~ 44,000 species. These comprise fascinating creatures with huge morphological and ecological disparity. Such great diversity comes with even larger phylogenetic uncertainty and many taxa have been largely neglected in molecular assessments. Genomic tools have provided resolution to deep cladogenic events but generating large numbers of transcriptomes/genomes is expensive and usually requires fresh material. Here we leverage a target enrichment approach to design and synthesize a probe set based on available genomes and transcriptomes across Heterobranchia. Our probe set contains 57,606 70mer baits and targets a total of 2,259 ultra-conserved elements (UCEs). Post-sequencing capture efficiency was tested against 31 marine heterobranchs from major groups, including Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida, Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura, up to 1,978 in Nudipleura, and up to 1,927 in Acteonoidea, the latter two being the most distantly related taxa to our core study group. Total alignment length was 525,599 bp and contained 52% informative sites and 21% missing data. Maximum-likelihood and Bayesian inference approaches recovered the monophyly of all orders tested as well as the larger clades Nudipleura, Panpulmonata, and Euopisthobranchia. The successful enrichment of diversely preserved material and DNA concentrations demonstrate the polyvalent nature of UCEs, and the universality of the probe set designed. We believe this probe set will enable multiple, interesting lines of research, that will benefit from an inexpensive and largely informative tool that will, additionally, benefit from the access to museum collections to gather genomic data.

Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly

Background

Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.

Results

We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.

Conclusions

TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.

Software, a detailed manual, and example data files are available through github carolinafishes.github.io

Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties

Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.

Male Alternative Reproductive Tactics and Associated Evolution of Anatomical Characteristics in Loliginid Squid

Loliginid squids provide a unique model system to explore male alternative reproductive tactics (ARTs) and their linkage to size, behavioral decision making, and possibly age. Large individuals fight one another and the winners form temporary consortships with females, while smaller individuals do not engage in male-male agonistic bouts but use various sneaker tactics to obtain matings, each with varying mating and fertilization success. There is substantial behavioral flexibility in most species, as smaller males can facultatively switch to the alternative consort behaviors as the behavioral context changes. These forms of ARTs can involve different: mating posture; site of spermatophore deposition; fertilization success; and sperm traits. Most of the traits of male dimorphism (both anatomical and behavioral) are consistent with traditional sexual selection theory, while others have unique features that may have evolved in response to the fertilization environment faced by each temporary or permanent male morph.

The Current State of Cephalopod Science and Perspectives on the Most Critical Challenges Ahead From Three Early-Career Researchers

Here, three researchers who have recently embarked on careers in cephalopod biology discuss the current state of the field and offer their hopes for the future. Seven major topics are explored: genetics, aquaculture, climate change, welfare, behavior, cognition, and neurobiology. Recent developments in each of these fields are reviewed and the potential of emerging technologies to address specific gaps in knowledge about cephalopods are discussed. Throughout, the authors highlight specific challenges that merit particular focus in the near-term. This review and prospectus is also intended to suggest some concrete near-term goals to cephalopod researchers and inspire those working outside the field to consider the revelatory potential of these remarkable creatures.