Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial.

The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories, and its tipping point may lie within the mitigated warming scenarios of 1.5° to 2°C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates could resolve this uncertainty, including the Last Interglacial when global sea levels were 5 to 10 meters higher than today and global average temperatures were 0.5° to 1.5°C warmer than preindustrial levels. Using a panel of genome-wide, single-nucleotide polymorphisms of a circum-Antarctic octopus, we show persistent, historic signals of gene flow only possible with complete WAIS collapse. Our results provide the first empirical evidence that the tipping point of WAIS loss could be reached even under stringent climate mitigation scenarios.

Trophic ecology of Octopus vulgaris paralarvae along the Iberian Canary current eastern boundary upwelling system.

Our knowledge of the diet of wild octopus paralarvae, Octopus vulgaris, is restricted to the first 2 weeks of its planktonic phase when they are selective hunters found near the coastline. These small paralarvae, bearing only three suckers per arm, are transported by oceanic currents from the coast towards offshore waters, where they complete the planktonic phase over 2 months. Here, we have investigated the trophic ecology of O. vulgaris paralarvae in two contrasting upwelling sub-regions of the Iberian Canary current (ICC) eastern boundary upwelling system and have evaluated dietary change as paralarvae develop (inferred by counting the number of suckers per arm, ranging from three to 15) along the coastal-oceanic gradient during their planktonic phase. Using high-throughput amplicon sequencing, we have characterised the diet of 100 paralarvae collected along the Northwest Iberian Peninsula (n = 65, three to five suckers per arm) and off the west coast of Morocco (n = 35, three to 15 suckers per arm), identifying up to 87 different prey species. The diet of paralarvae varied along the ICC, with crabs (53.4%), siphonophores (12.2%), copepods (12.3%), cnidarians (8.4%) and pteropods (3.7%) accounting for 90% of the variability detected off NW Iberian Peninsula, whereas off W Morocco, crabs (46.2%), copepods (23.1%), cnidarians (12.9%), krill (9.3%) and fishes (4.2%) explained 95.6% of the variability observed using frequency of observance (FOO%) data. Ontogenetic changes in the diet based on groups of paralarvae with similar numbers per arm were evidenced by the decreasing contribution of coastal meroplankton and an increase in oceanic holoplankton, including siphonophores, copepods, pteropods and krill. Trophic niche breadth values ranged from 0.06 to 0.67, with averaged values ranging from 0.23 to 0.33 (generalist = 1 and specialist = 0), suggesting that O. vulgaris paralarvae are selective predators through their ontogenetic transition between coastal and oceanic environments.

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 3 m to >100 m. 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 âˆ¼30 mya 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" (>100 m) 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.

Genomic insights of evolutionary divergence and life history innovations in Antarctic brittle stars.

Understanding the drivers of evolutionary innovation provides a crucial perspective of how evolutionary processes unfold across taxa and ecological systems. It has been hypothesised that the Southern Ocean provided ecological opportunities for novelty in the past. However, the drivers of innovation are challenging to pinpoint as the evolutionary genetics of Southern Ocean fauna are influenced by Quaternary glacial-interglacial cycles, oceanic currents and species ecology. Here we examined the genome-wide single nucleotide polymorphisms of the Southern Ocean brittle stars Ophionotus victoriae (five arms, broadcaster) and O. hexactis (six arms, brooder). We found that O. victoriae and O. hexactis are closely-related species with interspecific gene flow. During the late Pleistocene, O. victoriae likely persisted in a connected deep water refugium and in situ refugia on the Antarctic continental shelf and around Antarctic islands; O. hexactis persisted exclusively within in situ island refugia. Within O. victoriae, contemporary gene flow linking to the Antarctic Circumpolar Current, regional gyres and other local oceanographic regimes was observed. Gene flow connecting West and East Antarctic islands near the Polar Front was also detected in O. hexactis. A strong association was detected between outlier loci and salinity in O. hexactis. Both O. victoriae and O. hexactis are associated with genome-wide increase in alleles at intermediate-frequencies; the alleles associated with this peak appear to be species specific, and these intermediate-frequency variants are far more excessive in O. hexactis. We hypothesise that the peak in alleles at intermediate frequencies could be related to adaptation in the recent past, linked to evolutionary innovations of increase in arm number and a switch to brooding from broadcasting, in O. hexactis.

Disentangling genetic from environmental effects on phenotypic variability of southern rock lobster (Jasus edwardsii) postlarvae.

Environmental conditions experienced during the larval dispersal of marine organisms can determine the size-at-settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here, we investigated morphological differences in recently settled southern rock lobster (Jasus edwardsii) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction site-associated DNA sequencing (ddRADseq) to assess differences in the genetic structure of recently settled recruits on the east coast of Tasmania over 3 months of peak settlement during 2012 (August-October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller individuals found at the northernmost site. Also, there was a lack of overall genetic divergence; however, significant differences in pairwise FST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, individuals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic divergence in the presence of phenotypic variation indicates that larval environmental history during the dispersal of J. edwardsii could be a possible driver of the resulting phenotype of settlers.

Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum.

Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.

Diel Rhythm and Thermal Independence of Metabolic Rate in a Benthic Shark.

Biological rhythms that are mediated by exogenous factors, such as light and temperature, drive the physiology of organisms and affect processes ranging from cellular to population levels. For elasmobranchs (i.e. sharks, rays, and skates), studies documenting diel activity and movement patterns indicate that many species are crepuscular or nocturnal in nature. However, few studies have investigated the rhythmicity of elasmobranch physiology to understand the mechanisms underpinning these distinct patterns. Here, we assess diel patterns of metabolic rates in a small meso-predator, the epaulette shark (Hemiscyllium ocellatum), across ecologically relevant temperatures and upon acutely removing photoperiod cues. This species possibly demonstrates behavioral sleep during daytime hours, which is supported herein by low metabolic rates during the day and a 1.7-fold increase in metabolic rates at night. From spring to summer seasons, where average average water temperature temperatures for this species range 24.5 to 28.5 °C, time of day, and not temperature, had the strongest influence on metabolic rate. These results indicate that this species, and perhaps other similar species from tropical and coastal environments, may have physiological mechanisms in place to maintain metabolic rate on a seasonal time scale regardless of temperature fluctuations that are relevant to their native habitats.

Emerging biological archives can reveal ecological and climatic change in Antarctica.

Anthropogenic climate change is causing observable changes in Antarctica and the Southern Ocean including increased air and ocean temperatures, glacial melt leading to sea-level rise and a reduction in salinity, and changes to freshwater water availability on land. These changes impact local Antarctic ecosystems and the Earth's climate system. The Antarctic has experienced significant past environmental change, including cycles of glaciation over the Quaternary Period (the past ~2.6 million years). Understanding Antarctica's paleoecosystems, and the corresponding paleoenvironments and climates that have shaped them, provides insight into present day ecosystem change, and importantly, helps constrain model projections of future change. Biological archives such as extant moss beds and peat profiles, biological proxies in lake and marine sediments, vertebrate animal colonies, and extant terrestrial and benthic marine invertebrates, complement other Antarctic paleoclimate archives by recording the nature and rate of past ecological change, the paleoenvironmental drivers of that change, and constrain current ecosystem and climate models. These archives provide invaluable information about terrestrial ice-free areas, a key location for Antarctic biodiversity, and the continental margin which is important for understanding ice sheet dynamics. Recent significant advances in analytical techniques (e.g., genomics, biogeochemical analyses) have led to new applications and greater power in elucidating the environmental records contained within biological archives. Paleoecological and paleoclimate discoveries derived from biological archives, and integration with existing data from other paleoclimate data sources, will significantly expand our understanding of past, present, and future ecological change, alongside climate change, in a unique, globally significant region.

Is the Southern Ocean ecosystem primed for change or at the cliff edge?

The Southern Ocean is experiencing unprecedented environmental risks and consequences from current climate change. It is unclear how the benthic fauna, which has largely evolved in isolation, will respond to future changes. Knowing how the benthic fauna persisted through repeated extreme glacial-interglacial cycles in the past provides a unique opportunity to inform future predictions. Right now, understanding and preserving current genetic diversity and connectivity between populations will give species the best chance to adapt.

Development of an STR panel for a non-native population of an endangered species.

BACKGROUND: The establishment of non-native populations of threatened and legally protected species can have many implications for the areas where these species have been introduced. Non-native populations of threatened species have the potential to be exploited and therefore the subject of legal protection, while conversely, if they have become invasive in their introduced range, there is the likelihood that population control will be carried out to reduce abundance and negative impacts associated with introduced species. From both a legal and invasive species monitoring standpoint, it is important to know how many individuals are present. METHODS AND RESULTS: Short tandem repeats (STRs) were developed for the hog deer, an endangered species that was introduced following European settlement to Victoria, Australia using Illumina MiSeq sequencing technology. These markers were combined with previous STRs characterised for hog deer to create a 29-plex identification system. A total of 224 samples were genotyped across the population in Victoria, and further analyses of null allele frequencies, deviation from Hardy-Weinberg equilibrium, and the removal of monomorphic or low amplifying markers resulted in a final marker panel of 15 loci. Despite low values for number of alleles at each locus (2-4), probability of identity showed sufficient discrimination power, with an average probability of identity at 2.94 × 10-6, and a probability of sibling identity of 8.9 × 10-4 across all sites. CONCLUSIONS: It is feasible to create an informative DNA profiling system that can distinguish between individuals for applications in both wildlife forensic and population control research.

Evolutionary innovations in Antarctic brittle stars linked to glacial refugia.

The drivers behind evolutionary innovations such as contrasting life histories and morphological change are central questions of evolutionary biology. However, the environmental and ecological contexts linked to evolutionary innovations are generally unclear. During the Pleistocene glacial cycles, grounded ice sheets expanded across the Southern Ocean continental shelf. Limited ice-free areas remained, and fauna were isolated from other refugial populations. Survival in Southern Ocean refugia could present opportunities for ecological adaptation and evolutionary innovation. Here, we reconstructed the phylogeographic patterns of circum-Antarctic brittle stars Ophionotus victoriae and O. hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). We examined the evolutionary relationship between the two species using cytochrome c oxidase subunit I (COI) data. COI data suggested that O. victoriae is a single species (rather than a species complex) and is closely related to O. hexactis (a separate species). Since their recent divergence in the mid-Pleistocene, O. victoriae and O. hexactis likely persisted differently throughout glacial maxima, in deep-sea and Antarctic island refugia, respectively. Genetic connectivity, within and between the Antarctic continental shelf and islands, was also observed and could be linked to the Antarctic Circumpolar Current and local oceanographic regimes. Signatures of a probable seascape corridor linking connectivity between the Scotia Sea and Prydz Bay are also highlighted. We suggest that survival in Antarctic island refugia was associated with increase in arm number and a switch from broadcast spawning to brooding in O. hexactis, and propose that it could be linked to environmental changes (such as salinity) associated with intensified interglacial-glacial cycles.

Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations.

BACKGROUND: Globally, amphibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered "possibly extinct". Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for 'missing' and endangered amphibian populations by screening water samples from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances. METHODS: Here we tested downstream detection distances in two endangered stream frogs (Litoria lorica and L. nannotis) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L). RESULTS: We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most sampling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water samples, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs). DISCUSSION: The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species-indeed it was effective in this study-but we also achieved far-downstream detections when precipitating eDNA from 100 mL water samples. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances (>20 km) suggest eDNA is a valuable tool for detecting rare stream amphibians. We provide recommendations on optimal survey methods.

Climatic change drives dynamic source-sink relationships in marine species with high dispersal potential.

While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species-specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual-based model coupled with contemporary migration estimates inferred from genetic data showed stronger inter-ocean connectivity in the opposite direction from the Atlantic to the Indian Ocean driven by the Subtropical Front. We suggest that the J. tristani and J. paulensis historical distribution might have extended further north (when water temperatures were lower) resulting in larval dispersal between the ocean basis being more influenced by the Agulhas Leakage than the Subtropical Front. As water temperatures in the region increase in accordance with anthropogenic climate change, a southern shift in the distribution range of J. tristani and J. paulensis could further reduce larval transport from the Indian to the Atlantic Ocean, adding complexity to fisheries management.

Global drivers of recent diversification in a marine species complex.

Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40o S. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST ), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

ampir: an R package for fast genome-wide prediction of antimicrobial peptides.

SUMMARY: Antimicrobial peptides (AMPs) are the key components of the innate immune system that protect against pathogens, regulate the microbiome and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. AVAILABILITY AND IMPLEMENTATION: ampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://github.com/legana/ampir. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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.

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.

Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.

The shell matrix and microstructure of the Ram's Horn squid: Molecular and structural characterization.

Molluscs are one of the most diversified phyla among metazoans. Most of them produce an external calcified shell, resulting from the secretory activity of a specialized epithelium of the calcifying mantle. This biomineralization process is controlled by a set of extracellular macromolecules, the organic matrix. In spite of several studies, these components are mainly known for bivalves and gastropods. In the present study, we investigated the physical and biochemical properties of the internal planispiral shell of the Ram's Horn squid Spirula spirula. Scanning Electron Microscope investigations of the shell reveal a complex microstructural organization. The saccharides constitute a quantitatively important moiety of the matrix, as shown by Fourier-transform infrared and solid-state nuclear magnetic resonance spectroscopies. NMR identified ß-chitin and additional polysaccharides for a total amount of 80% of the insoluble fraction. Proteomics was applied to both soluble and insoluble matrices and in silico searches were performed, first on heterologous metazoans models, and secondly on an unpublished transcriptome of Spirula spirula. In the first case, several peptides were identified, some of them matching with tyrosinase, chitinase 2, protease inhibitor, or immunoglobulin. In the second case, 39 hits were obtained, including transferrin, a serine protease inhibitor, matrilin, or different histones. The very few similarities with known molluscan shell matrix proteins suggest that Spirula spirula uses a unique set of shell matrix proteins for constructing its internal shell. The absence of similarity with closely related cephalopods demonstrates that there is no obvious phylogenetic signal in the cephalopod skeletal matrix.

A biogeographic framework of octopod species diversification: the role of the Isthmus of Panama.

The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America and caused the separation of the Western Atlantic and Eastern Pacific oceans, resulting in profound changes in the environmental and oceanographic conditions. To evaluate how these changes have influenced speciation processes in octopods, fragments of two mitochondrial (Cytochrome oxidase subunit I, COI and 16S rDNA) and two nuclear (Rhodopsin and Elongation Factor-1α, EF-1α) genes were amplified from samples from the Atlantic and Pacific oceans. One biogeographical and four fossil calibration priors were used within a relaxed Bayesian phylogenetic analysis framework to estimate divergence times among cladogenic events. Reconstruction of the ancestral states in phylogenies was used to infer historical biogeography of the lineages and species dispersal routes. The results revealed three well-supported clades of transisthmian octopus sister species pair/complex (TSSP/TSSC) and two additional clades showing a low probability of species diversification, having been influenced by the IP. Divergence times estimated in the present study revealed that octopod TSSP/TSSC from the Atlantic and Pacific diverged between the Middle Miocene and Early Pliocene (mean range = 5-18 Ma). Given that oceanographic changes caused by the uplift of the IP were so strong as to affect the global climate, we suggest that octopod TSSP/TSSC diverged because of these physical and environmental barriers, even before the complete uplift of the IP 3 Ma, proposed by the Late Pliocene model. The results obtained in this phylogenetic reconstruction also indicate that the octopus species pairs in each ocean share a recent common ancestor from the Pacific Ocean.