Rates of population differentiation and speciation are decoupled in sea snakes

Anti-predator defences are linked with high levels of genetic differentiation in frogs

Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

Sexual dimorphism in aipysurine sea snakes (Elapidae, Hydrophiinae)

The transition from terrestrial to aquatic life by hydrophiine elapid snakes modified targets of natural selection and likely affected sexual selection also. Thus, the shift to marine life also might have affected sexual dimorphism. Our measurements of 419 preserved specimens of six species of aipysurine snakes (genera Emydocephalus and Aipysurus) revealed sexual dimorphism in mean adult snout-vent length (SVL), body width relative to SVL, lengths and widths of heads and tails relative to SVL, and eye diameter relative to head length. Females averaged larger than males in all taxa, and generally were wider-bodied with shorter and wider tails and smaller eyes. For other traits, sexual dimorphism varied among species: for example, relative head length ranged from male-biased to female-biased, and head shape (width relative to length) was highly dimorphic only in A. laevis. The transition to marine life may have eliminated male-male combat (reducing selection for large males) and favoured visual rather than pheromone-based mate-searching (favouring larger eyes in males). Variation in head-size dimorphism may reflect intersexual niche partitioning, with different taxa following different trajectories. Repeated evolutionary transitions from terrestrial to aquatic life in snakes provide a powerful opportunity to explore selective forces on sexually dimorphic traits.

Macroevolution in axial morphospace: innovations accompanying the transition to marine environments in elapid snakes

Sea snakes in the Hydrophis-Microcephalophis clade (Elapidae) show exceptional body shape variation along a continuum from similar forebody and hindbody girths, to dramatically reduced girths of the forebody relative to hindbody. The latter is associated with specializations on burrowing prey. This variation underpins high sympatric diversity and species richness and is not shared by other marine (or terrestrial) snakes. Here, we examined a hypothesis that macroevolutionary changes in axial development contribute to the propensity, at clade level, for body shape change. We quantified variation in the number and size of vertebrae in two body regions (pre- and post-apex of the heart) for approximately 94 terrestrial and marine elapids. We found Hydrophis-Microcephalophis exhibit increased rates of vertebral evolution in the pre- versus post-apex regions compared to all other Australasian elapids. Unlike other marine and terrestrial elapids, axial elongation in Hydrophis-Microcephalophis occurs via the preferential addition of vertebrae pre-heart apex, which is the region that undergoes concomitant shifts in vertebral number and size during transitions along the relative fore- to hindbody girth axis. We suggest that this macroevolutionary developmental change has potentially acted as a key innovation in Hydrophis-Microcephalophis by facilitating novel (especially burrowing) prey specializations that are not shared with other marine snakes.

Dispersal ability and its consequences for population genetic differentiation and diversification

Dispersal ability is known to influence geographical structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary timescales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.

Divergence in life-history traits among three adjoining populations of the sea snake Emydocephalus annulatus (Hydrophiinae, Elapidae)

Life-history traits such as rates of growth, survival and reproduction can vary though time within a single population, or through space among populations, due to abiotically-driven changes in resource availability. In terrestrial reptiles, parameters such as temperature and rainfall generate variation in life-histories—but other parameters likely are more important in marine systems. We studied three populations of sea snakes (Emydocephalus annulatus) in adjacent bays in the IndoPacific archipelago of New Caledonia. The extreme philopatry of individual snakes allows us to unambiguously allocate each animal to one of the three populations. Although water temperatures and rainfall do not differ over this small scale, one site experiences more intense winds, restricting opportunities for foraging. Our 18-year mark-recapture dataset (> 1,200 snakes, > 2,400 captures) reveals significant divergence among populations in life-history traits. Survival rates and population densities were similar among sites, but snakes at the most wind-exposed site (Anse Vata) exhibited lower body condition, slower growth, less frequent production of litters, and smaller litters. Weather-driven variation in feeding rates thus may affect life-history traits of marine snakes as well as their terrestrial counterparts, but driven by different parameters (e.g., wind exposure rather than variation in temperatures or rainfall).

Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences

The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. Here, we compared the population histories of marine and terrestrial elapid snakes using the pairwise sequentially Markovian coalescent (PSMC) model to track historical fluctuations in species' effective population sizes (N_e ) from individual whole-genome sequences. To do this we generated a draft genome for the olive sea snake (Aiysurus laevis) and analysed this alongside six published elapid genomes and their sequence reads (marine species Hydrophis curtus, H. melanocephalus and Laticauda laticaudata; terrestrial species Pseudonaja textilis, Naja Naja and Notechis scutatus). Counter to the expectation that marine species should show higher overall N_e and less pronounced fluctuations in N_e , our analyses reveal demographic patterns that are highly variable among species and do not clearly correspond to major ecological divisions. At deeper time intervals, the four marine elapids appear to have experienced relatively stable N_e , while each terrestrial species shows a prominent upturn in N_e starting at ~4 million years ago (Ma) followed by an equally strong decline. However, over the last million years, all seven species show strong and divergent fluctuations. Estimates of N_e in the most recent intervals (~10 kya) are lowest in two of four marine species (H. melanocephalus and Laticauda), and do not correspond to contemporary range sizes in marine or terrestrial taxa.

New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes

Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway “Circadian Entrainment.” This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.

Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes

Dermal phototaxis has been reported in a few aquatic vertebrate lineages spanning fish, amphibians and reptiles. These taxa respond to light on the skin of their elongate hind-bodies and tails by withdrawing under cover to avoid detection by predators. Here, we investigated tail phototaxis in sea snakes (Hydrophiinae), the only reptiles reported to exhibit this sensory behaviour. We conducted behavioural tests in 17 wild-caught sea snakes of eight species by illuminating the dorsal surface of the tail and midbody skin using cold white, violet, blue, green and red light. Our results confirmed phototactic tail withdrawal in the previously studied Aipysurus laevis, revealed this trait for the first time in A. duboisii and A. tenuis, and suggested that tail photoreceptors have peak spectral sensitivities between blue and green light (457-514 nm). Based on these results, and an absence of photoresponses in five Aipysurus and Hydrophis species, we tentatively infer that tail phototaxis evolved in the ancestor of a clade of six Aipysurus species (comprising 10% of all sea snakes). Quantifying tail damage, we found that the probability of sustaining tail injuries was not influenced by tail phototactic ability in snakes. Gene profiling showed that transcriptomes of both tail skin and body skin lacked visual opsins but contained melanopsin (opn4x) in addition to key genes of the retinal regeneration and phototransduction cascades. This work suggests that a nonvisual photoreceptor (e.g., Gq rhabdomeric) signalling pathway underlies tail phototaxis, and provides candidate gene targets for future studies of this unusual sensory innovation in reptiles.

Rates of population differentiation and speciation are decoupled in sea snakes

Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographical population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography across northern Australia in 16 species from two closely related clades that show contrasting diversification dynamics. Contrary to expectations from theory and several empirical studies, our results show that, at the geographical scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographical structure. By contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have threefold slower speciation rates. Alternative factors, such as ecological specialization, species duration and geographical range size, may underlie rapid speciation in sea snakes.