Reproductive modes of the South American water snakes: A study system for the evolution of viviparity in squamate reptiles

A synthetic review: natural history of amniote reproductive modes in light of comparative evolutionary genomics

There is a current lack of consensus on whether the ancestral parity mode was oviparity (egg-laying) or viviparity (live-birth) in amniotes and particularly in squamates (snakes, lizards, and amphisbaenids). How transitions between parity modes occur at the genomic level has primary importance for how science conceptualises the origin of amniotes, and highly variable parity modes in Squamata. Synthesising literature from medicine, poultry science, reproductive biology, and evolutionary biology, I review the genomics and physiology of five broad processes (here termed the 'Main Five') expected to change during transitions between parity modes: eggshell formation, embryonic retention, placentation, calcium transport, and maternal-fetal immune dynamics. Throughout, I offer alternative perspectives and testable hypotheses regarding proximate causes of parity mode evolution in amniotes and squamates. If viviparity did evolve early in the history of lepidosaurs, I offer the nucleation site hypothesis as a proximate explanation. The framework of this hypothesis can be extended to amniotes to infer their ancestral state. I also provide a mechanism and hypothesis on how squamates may transition from viviparity to oviparity and make predictions about the directionality of transitions in three species. After considering evidence for differing perspectives on amniote origins, I offer a framework that unifies (i) the extended embryonic retention model and (ii) the traditional model which describes the amniote egg as an adaptation to the terrestrial environment. Additionally, this review contextualises the origin of amniotes and parity mode evolution within Medawar's paradigm. Medawar posited that pregnancy could be supported by immunosuppression, inertness, evasion, or immunological barriers. I demonstrate that this does not support gestation or gravidity across most amniotes but may be an adequate paradigm to explain how the first amniote tolerated internal fertilization and delayed egg deposition. In this context, the eggshell can be thought of as an immunological barrier. If serving as a barrier underpins the origin of the amniote eggshell, there should be evidence that oviparous gravidity can be met with a lack of immunological responses in utero. Rare examples of two species that differentially express very few genes during gravidity, suggestive of an absent immunological reaction to oviparous gravidity, are two skinks Lampropholis guichenoti and Lerista bougainvillii. These species may serve as good models for the original amniote egg. Overall, this review grounds itself in the historical literature while offering a modern perspective on the origin of amniotes. I encourage the scientific community to utilise this review as a resource in evolutionary and comparative genomics studies, embrace the complexity of the system, and thoughtfully consider the frameworks proposed.

Whole Genome Assembly and Annotation of Blackstripe Livebearer Poeciliopsis prolifica

The blackstripe livebearer Poeciliopsis prolifica is a live-bearing fish belonging to the family Poeciliidae with high level of postfertilization maternal investment (matrotrophy). This viviparous matrotrophic species has evolved a structure similarly to the mammalian placenta. Placentas have independently evolved multiple times in Poeciliidae from nonplacental ancestors, which provide an opportunity to study the placental evolution. However, there is a lack of high-quality reference genomes for the placental species in Poeciliidae. In this study, we present a 674 Mb assembly of P. prolifica in 504 contigs with excellent continuity (contig N50 7.7 Mb) and completeness (97.2% Benchmarking Universal Single-Copy Orthologs [BUSCO] completeness score, including 92.6% single-copy and 4.6% duplicated BUSCO score). A total of 27,227 protein-coding genes were annotated from the merged datasets based on bioinformatic prediction, RNA sequencing and homology evidence. Phylogenomic analyses revealed that P. prolifica diverged from the guppy (Poecilia reticulata) ∼19 Ma. Our research provides the necessary resources and the genomic toolkit for investigating the genetic underpinning of placentation.

Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

A 50-year-old redescription: molecular and morphometric characterization of Hepatozoon carinicauda Pessôa and Cavalheiro, 1969 in the brown-banded water snake Helicops angulatus (Linnaeus, 1758)

The combined use of molecular and microscopic techniques has become an increasingly common and efficient practice for the taxonomic and evolutionary understanding of single-celled parasites such as haemogregarines. Based on this integrative approach, we characterized Hepatozoon found in Helicops angulatus snakes from the Eastern Amazonia, Brazil. The gamonts observed caused cell hypertrophy and were extremely elongated and, in some cases, piriform (mean dimensions: 25.3 ± 1.9 × 8.6 ± 1.3 μm). These morphological features correspond to Hepatozoon carinicauda, described 50 years ago in the snake Helicops carinicaudus in the southeast region of Brazil. Phylogenetic and genetic divergence analyses, performed with the sequence obtained from the amplification of a 590 bp fragment of the 18S rRNA gene, revealed that Hepatozoon in He. angulatus differed from the other lineages retrieved from GenBank, and was clustered singly in both the phylogenetic tree and the haplotype network. The integration of these data allowed the identification of H. carinicauda in a new aquatic host, and increased the knowledge of its geographical distribution. Therefore, the present study included the first redescription of a Hepatozoon species in a snake from the Brazilian Amazon.

Understanding the evolution of viviparity using intraspecific variation in reproductive mode and transitional forms of pregnancy

How innovations such as vision, flight and pregnancy evolve is a central question in evolutionary biology. Examination of transitional (intermediate) forms of these traits can help address this question, but these intermediate phenotypes are very rare in extant species. Here we explore the biology and evolution of transitional forms of pregnancy that are midway between the ancestral state of oviparity (egg-laying) and the derived state, viviparity (live birth). Transitional forms of pregnancy occur in only three vertebrates, all of which are lizard species that also display intraspecific variation in reproductive phenotype. In these lizards (Lerista bougainvillii, Saiphos equalis, and Zootoca vivipara), geographic variation of three reproductive forms occurs within a single species: oviparity, viviparity, and a transitional form of pregnancy. This phenomenon offers the valuable prospect of watching 'evolution in action'. In these species, it is possible to conduct comparative research using different reproductive forms that are not confounded by speciation, and are of relatively recent origin. We identify major proximate and ultimate questions that can be addressed in these species, and the genetic and genomic tools that can help us understand how transitional forms of pregnancy are produced, despite predicted fitness costs. We argue that these taxa represent an excellent prospect for understanding the major evolutionary shift between egg-laying and live birth, which is a fundamental innovation in the history of animals.

Taxonomy, allometry, sexual dimorphism, and conservation of the trans-Andean watersnake Helicops danieli Amaral, 1937 (Serpentes: Dipsadidae: Hydropsini)

The extensive lack of knowledge on the morphological aspects of South American watersnakes includes a poor understanding of phenotypic parameters, intraspecific variation, and conservation of the trans-Andean Helicops species, Daniel’s Keelback (Helicops danieli Amaral, 1937). For the first time, we provide a multidisciplinary view using key features (e.g., morphology and niche modeling) to improve the taxonomic recognition of this species, as well as describing ontogenetic color changes, allometry, sexual dimorphism, and the conservation status of this poorly studied snake. First, we emended the morphological diagnosis of H. danieli with 23 characters and detected that juvenile tail length is positively related to allometric growth, and that juveniles differ from adults through the presence of the white nuchal collar. Females are larger than males for snout–vent length, whereas males showed proportionally longer tails and smaller head length growth. Suitable areas for H. danieli are restricted to the trans-Andean regions from the Magdalena drainage to the Caribbean coast, which also showed high values of anthropic impacts. Our multidisciplinary approach provided new insights into this South American watersnake’s morphology, intraspecific variation, and distribution.

Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation

The Atlantic Forest is one of the largest and richest tropical rainforests on the planet, being one of the 25 world priorities for conservation. The Atlantic Forest portion located north of the São Francisco River corresponds to the Pernambuco Endemism Center (PEC). We describe the snake composition of the PEC, providing information about the diversity, natural history and geographical distribution of the species, based on records from five scientific collections and additional information from the literature. A total of 78 species of snakes distributed in eight families was registered in the Pernambuco Endemism Center. The Caatinga is the Brazilian biome that most shares species with the PEC, followed by Cerrado. On the other hand, seven species are considered endemic of this region. Most of the snake species in the PEC have been registered in forest (94.8%), followed by “Brejos Nordestinos” (46.1%), Tabuleiros (43.5%), Restingas (14.1%) and Mangroves (5.1%). The PEC snake fauna includes mainly terrestrial species (60.2%) and cryptozoic and/or fossorial species (21.7%), but also presents a high richness of semi-arboreal and arboreal species (29.5%). Vertebrates are the main food item consumed by the species (78% of species), among the main prey are mammals, lizards, and amphibians. Most species show a strictly nocturnal activity period (50%), followed by strictly diurnal (38%). The PEC is the most degraded and least known region of the Atlantic Forest, yet it has revealed a high richness of snake species, including seven endemic species. It is emphasized that regional conservation efforts need to be intensified, because few forests in the region are formally protected, and the majority consist of small and poorly protected fragments, which means that many species in the region may be in risk of extinction.

Notes on court and copula, fertility, nest, eggs and hatchlings of the Caatinga's black snake Boiruna sertaneja Zaher, 1996 (Serpentes: Dipsadidae) from northeastern Brazil

The Caatinga's black snake Boiruna sertaneja is a Pseudoboini species, endemic of the Caatinga biome. It is rare and fits in five traits that suggest it deserve more attention in reproduction research and conservation policies. Here we provide information on reproductive biology of B. sertaneja by adding new data about court and copula, fertility, nest, eggs and hatchling morphometry and pattern of color based on captivity specimens. The court and copula, as well as oviposition of B. sertaneja in the Caatinga are associated to period of high temperature and dry season. Our findings indicate that females of B. sertaneja, in nature, could select protected places or actively build their nests. We recorded three oviposture after a single event of copula by the female of B. sertaneja. The long time gap between copula and clutches strongly suggests that female B. sertaneja can store sperm in their oviducts for long periods or do facultative parthenogenesis. Clutch size and hatchling size of B. sertaneja was high. We observed variation on the pattern of coloration among hatchlings of same litter. This study comprises the first description of important aspects of reproduction and can give us some clues about how B. sertaneja reproduce in nature.

Facultative oviparity in a viviparous skink ( Saiphos equalis)

Facultative changes in parity mode (oviparity to viviparity and vice versa) are rare in vertebrates, yet offer fascinating opportunities to investigate the role of reproductive lability in parity mode evolution. Here, we report apparent facultative oviparity by a viviparous female of the bimodally reproductive skink Saiphos equalis-the first report of different parity modes within a vertebrate clutch. Eggs oviposited facultatively possess shell characteristics of both viviparous and oviparous S. equalis, demonstrating that egg coverings for viviparous embryos are produced by the same machinery as those for oviparous individuals. Since selection may act in either direction when viviparity has evolved recently, squamate reproductive lability may confer a selective advantage. We suggest that facultative oviparity is a viable reproductive strategy for S. equalis and that squamate reproductive lability is more evolutionarily significant than previously acknowledged.

Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes

Mechanisms leading to sympatric speciation are diverse and may build up reproductive isolation. Reproductive isolation among differentiated clades may exist due to genetic incompatibilities, sexual selection, differences in parity mode, reduced post-zygotic survival or reproductive success of hybrids. Here, we test whether differences in parity mode lead to reproductive isolation by investigating introgression in Zootoca vivipara, a lizard species exhibiting oviparous and viviparous reproduction. We measured introgression in transects spanning different viviparous clades, different oviparous subclades, transects containing oviparous and viviparous clades, and transects within the same subclade (control transects). Introgression in transects spanning oviparous and viviparous clades was one order of magnitude smaller than transects spanning the same reproductive mode and no statistical differences existed between transects spanning the same reproductive mode and control transects. Among types of transects, no significant differences existed in genetic and geographic distances, nor number of detected alleles. Moreover, hybrids were detected in all types of transects, showing that parity mode alone does not necessarily lead to complete reproductive isolation, which suggests that reinforcement may play an important role. The evolution of different parity modes together with reinforcement may thus promote reproductive isolation and rapid speciation, potentially explaining why only six of the almost 40,000 vertebrates belonging to groups consisting of viviparous and oviparous species exhibit bimodal reproduction.

The genetics of egg retention and fertilization success in Drosophila: One step closer to understanding the transition from facultative to obligate viviparity

Oviparous, facultative egg retention enables Drosophila females to withhold fertilized eggs in their reproductive tracts until circumstances favor oviposition. The propensity to retain fertilized eggs varies greatly between species, and is correlated with other reproductive traits, such as egg size and ovariole number. While previous studies have described the phenomenon, no study to date has characterized within-species variation or the genetic basis of the trait. Here, we develop a novel microscope-based method for measuring egg retention in Drosophila females and determine the range of phenotypic variation in mated female egg retention in a subset of 91 Drosophila Genetic Reference Panel (DGRP) lines. We inferred the genetic basis of egg retention using a genome-wide association study (GWAS). Further, the scoring of more than 95,000 stained, staged eggs enabled estimates of fertilization success for each line. We found evidence that ovary- and spermathecae-related genes as well as genes affecting olfactory behavior, male mating behavior, male-female attraction and sperm motility may play a crucial role in post-mating physiology. Based on our findings we also propose potential evolutionary routes toward obligate viviparity. In particular, we propose that the loss of fecundity incurred by viviparity could be offset by benefits arising from enhanced mate discrimination, resource specialization, or modified egg morphology.