Transitions in sex determination and sex chromosomes across vertebrate species

Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex-determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown whether there are convergent trends in the directionality of turnover in sex-determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex-determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles and amphibians. Contrary to theoretical predictions, we find no evidence that the evolution of separate sexes is irreversible, as transitions from separate sexes to hermaphroditism occur at higher rates than the reverse in fish. We also find that transitions from environmental sex determination to genetic sex determination occur at higher rates than the reverse in both squamates and fish, suggesting that genetic sex determination is more stable. However, our data are not consistent with the hypothesis that heteromorphic sex chromosomes are an "evolutionary trap." Rather, we find similar transition rates between homomorphic and heteromorphic sex chromosomes in both fish and amphibians, and to environmental sex determination from heteromorphic vs. homomorphic sex chromosome systems in fish. Finally, we find that transitions between male and female heterogamety occur at similar rates in amphibians and squamates, while transitions to male heterogamety occur at higher rates in fish. Together, these results provide the most comprehensive view to date of the evolution of vertebrate sex determination in a phylogenetic context, providing new insight into long-standing questions about the evolution of sexual reproduction.

Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches-anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)-and both approaches have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness and suggest areas for future improvement.

SquamataBase: a natural history database and R package for comparative biology of snake feeding habits

Public databases in taxonomy, phylogenetics and geographic and fossil occurrence records are key research tools that provide raw materials, on which broad-scale analyses and synthesis in their respective fields are based. Comparable repositories for natural history observations are rare. Publicly available natural history data on traits like diet, habitat and reproduction are scattered across an extensive primary literature and remain relatively inaccessible to researchers interested in using these data for broad-scale analyses in macroecology and macroevolution. In this paper, I introduce SquamataBase, an open-source R package and database of predator-prey records involving the world’s snakes. SquamataBase facilitates the discovery of natural history observations for use in comparative analyses and synthesis and, in its current form, contains observations of at least 18,304 predator individuals comprising 1,227 snake species and at least 58,633 prey items comprising 3,231 prey taxa. To facilitate integration with comparative analysis workflows, the data are distributed inside an R package, which also provides basic functionality for common data manipulation and filtering operations. Moving forward, the continued development of public natural history databases and their integration with existing digitisation efforts in biodiversity science should become a priority.

Evolutionary bedfellows: Reconstructing the ancestral state of autotomy and regeneration

Some form of regeneration occurs in all lifeforms and extends from single-cell organisms to humans. The degree to which regenerative ability is distributed across different taxa, however, is harder to ascertain given the potential for phylogenetic constraint or inertia, and adaptive processes to shape this pattern. Here, we examine the phylogenetic history of regeneration in two groups where the trait has been well-studied: arthropods and reptiles. Because autotomy is often present alongside regeneration in these groups, we performed ancestral state reconstructions for both traits to more precisely assess the timing of their origins and the degree to which these traits coevolve. Using an ancestral trait reconstruction, we find that autotomy and regeneration were present at the base of the arthropod and reptile trees. We also find that when autotomy is lost it does not re-evolve easily. Lastly, we find that the distribution of regeneration is intimately connected to autotomy with the association being stronger in reptiles than in arthropods. Although these patterns suggest that decoupling autotomy and regeneration at a broad phylogenetic scale may be difficult, the available data provides useful insight into their entanglement. Ultimately, our reconstructions provide the important groundwork to explore how selection may have played a role during the loss of regeneration in specific lineages.

Evolutionary origins of viviparity consistent with palaeoclimate and lineage diversification

It is of fundamental importance for the field of evolutionary biology to understand when and why major evolutionary transitions occur. Live-bearing young (viviparity) is a major evolutionary change and has evolved from egg-laying (oviparity) independently in many vertebrate lineages and most abundantly in lizards and snakes. Although contemporary viviparous squamate species generally occupy cold climatic regions across the globe, it is not known whether viviparity evolved as a response to cold climate in the first place. Here, we used available published time-calibrated squamate phylogenies and parity data on 3,498 taxa. We compared the accumulation of transitions from oviparity to viviparity relative to background diversification and a simulated binary trait. Extracting the date of each transition in the phylogenies and informed by 65 my of global palaeoclimatic data, we tested the nonexclusive hypotheses that viviparity evolved under the following: (a) cold, (b) long-term stable climatic conditions and (c) with background diversification rate. We show that stable and long-lasting cold climatic conditions are correlated with transitions to viviparity across squamates. This correlation of parity mode and palaeoclimate is mirrored by background diversification in squamates, and simulations of a binary trait also showed a similar association with palaeoclimate, meaning that trait evolution cannot be separated from squamate lineage diversification. We suggest that parity mode transitions depend on environmental and intrinsic effects and that background diversification rate may be a factor in trait diversification more generally.

Brain Allometry Across Macroevolutionary Scales in Squamates Suggests a Conserved Pattern in Snakes

Despite historical interest in brain size evolution in vertebrates, few studies have assessed variation in brain size in squamate reptiles such as snakes and lizards. Here, we analyzed the pattern of brain allometry at macroevolutionary scale in snakes and lizards, using body mass and snout vent length as measures of body size. We also assessed potential energetic trade-offs associated with relative brain size changes in Crotalinae vipers. Body mass showed a conserved pattern of brain allometry across taxa of snakes, but not in lizards. Body length favored changes of brain allometry in both snakes and lizards, but less variability was observed in snakes. Moreover, we did not find evidence for trade-offs between brain size and the size of other organs in Crotalinae. Thus, despite the contribution of body elongation to changes in relative brain size in squamate reptiles, snakes present low variation in brain allometry across taxa. Although the mechanisms driving this conserved pattern are unknown, we hypothesize that the snake body plan plays an important role in balancing the energetic demands of brain and body size increase at macroevolutionary scales. We encourage future research on the evolution of brain and body size in snakes to test this hypothesis.

Spatiotemporal distribution of neural crest cells in the common wall lizard Podarcis muralis

BACKGROUND

Neural crest cells (NCCs) are migratory embryonic stem cells that give rise to a diverse set of cell types. Here we describe the dynamic distribution of NCCs in developing embryos of the common wall lizard Podarcis muralis inferred from 10 markers. Our aim is to provide insights into the NCC development of lacertid lizards and to infer evolutionary modifications by comparisons to other tetrapods.

RESULTS

NCC migration is ongoing at oviposition, following three streams in the head and multiple in the trunk. From 21ss, we observe expression patterns indicating the beginning of differentiation toward mesenchymal and neuronal fates. By 35ss, migration is restricted to caudal levels, and fully differentiated chromaffin cells are observed.

CONCLUSIONS

We find that some markers show patterns that differ from other tetrapods. For example, the antibody HNK-1 labels three NCC streams from the hindbrain while some comparable reptile studies describe four. However, the information emerging from all markers combined shows that the overall spatiotemporal distribution of NCCs in the common wall lizard is largely conserved with that of other tetrapods. Our study highlights the dynamic nature of seemingly canonical marker genes and provides the first description of spatiotemporal NCC dynamics in a lacertid lizard.