Updated molecular phylogeny of the squid family Ommastrephidae: Insights into the evolution of spawning strategies

Gene Rearrangements in the Mitochondrial Genome of Gonatopsis borealis and Onychoteuthis compacta Reveal Their Phylogenetic Implications for Oegopsida

The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.

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.

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.

A phylogenetic approach to understand the evolution of reproduction in coleoid cephalopods

A central question in the evolution of life-histories is whether organisms reproduce once or repeatedly. For cephalopods, the main differences between semelparous and iteroparous are based on ovulation pattern and spawning type. The different reproductive strategies in coleoid cephalopods could be related to the habitat in which the species dwell (coastal vs. oceanic) and/or to environmental forces, thus, both aspects should be quantitatively evaluated under an evolutionary perspective to reconstruct: (a) the ancestral ovulation type of coleoid cephalopods, and (b) the potential of correlated evolution between ovulation type versus habitat and environment. Ancestral states of ovulation type were estimated using stochastic mapping based on literature data (i.e. synchronous or asynchronous), and this information was combined with a new molecular phylogeny including 165 species. The evolutionary correlation between ovulation type, habitat, and environment was estimated by means of the Markov model comparing the rates of gain and loss. The estimates of ancestral states of ovulation type for coleoid cephalopods resulted in a high probability that Octopodiformes evolved from synchronous ovulation type, and Decapodiformes from asynchronous ovulation type. The three traits evaluated presented phylogenetic signal, although no correlation was found between habitat and ovulation type. Overall, species in stable environments showed a tendency towards synchronous ovulation type, while the asynchronous ovulation pattern was found more frequently in species that live in unstable environments, being this last trait also responsible for triggering the change of ovulation type in some species throughout evolution.

Global biodiversity of the genus Ommastrephes (Ommastrephidae: Cephalopoda): an allopatric cryptic species complex

Cryptic speciation among morphologically homogeneous species is a phenomenon increasingly reported in cosmopolitan marine invertebrates. This situation usually leads to the discovery of new species, each of which occupies a smaller fraction of the original distributional range. The resolution of the taxonomic status of species complexes is essential because species are used as the unit of action for conservation and natural resource management politics. Before the present study, Ommastrephes bartramii was considered a monotypic cosmopolitan species with a discontinuous distribution. Here, individuals from nearly its entire distributional range were evaluated with mitochondrial DNA (cytochrome c oxidase subunit I and 16S rRNA). Four distinct species were consistently identified using four molecular species delimitation methods. These results, in combination with morphological and metabolic information from the literature, were used to resurrect three formerly synonymized names (Ommastrephes brevimanus, Ommastrephes caroli and Ommastrephes cylindraceus) and to propose revised distributional ranges for each species. In addition, diagnostic characters from the molecular sequences were incorporated in the species description. At present, only one of the four newly recognized species (Ommastrephes bartramii) is commercially exploited by fisheries in the North Pacific, but it now appears that the distributional range of this species is far smaller than previously believed, which is an essential consideration for effective fisheries management.

Sexual Selection and the Evolution of Male Reproductive Traits in Benthic Octopuses

Competition between same-sex organisms, or intra-sexual selection, can occur before and after mating, and include processes such as sperm competition and cryptic female choice. One of the consequences of intra-sexual selection is that male reproductive traits tend to evolve and diverge at high rates. In benthic octopuses, females often mate with more than one male in a single reproductive event, opening the venue for intra-sexual selection at multiple levels. For instance, males transfer spermatophores through hectocotylus, and can remove the spermatophores left by other males. Considering the limited evidence on post-copula competition in benthic octopuses, and the potential to affect the evolution of reproductive traits within octopodids, we put this hypothesis to a test employing a phylogenetic comparative approach. We combined data on hectocotylized arm length (HAL), ligula length (LL), spermatophore length (SL) with a Bayesian molecular phylogeny of 87 species, to analyze how reproductive traits have diverged across lineages and covary with body size (mantle length; ML). First, additionally to ML, we estimated the phylogenetic signal (λ) and mode of evolution (κ) in each reproductive trait. Second, we performed phylogenetic regressions to quantify the association among reproductive traits and their co-variation with ML. This analysis allowed us to estimate the phenotypic change along a branch into the phylogeny, and whether selection may have played a role in the evolution and diversification of specific clades. Estimations of λ were always high (>0.75), indicating concordance between the traits and the topology of the phylogenetic tree. Low values of κ (<1.0) suggested that evolution depends on branch lengths. All reproductive traits exhibiting a positive relation with ML (β > 0.5 in all cases). Overall, evolutionary rate models applied to the SL-ML regression suggested that octopuses of the family Megaleledonidae have evolved larger spermatophores than expected for their size. The regression HAL-ML indicated that HAL was more variable in Megaleledonidae than in the remaining clades, suggesting that the high divergence across species within this group might partially reflect intra-sexual selection. These results support the hypothesis that, at least in some lineages, sexual selection may account for the divergence in reproductive traits of male octopuses.