The Reptile Gut Microbiome: Its Role In Host Evolution And Community Assembly

I characterize the endogenous (gut) microbiome of Squamate reptiles, with a particular focus on the suborder Serpentes, and investigate the influence of the microbiome on host evolution and community assembly using samples I collected across three continents in the New and Old World. I developed novel methods for sampling the microbiomes of reptiles and summarized the current literature on non-mammalian gut microbiomes. In addition to establishing a standardized method of collecting and characterizing reptile microbiomes I made novel contributions to the future direction of the burgeoning field of host-associated microbiome research. Through persistent and rigorous fieldwork I amassed the largest dataset of non-mammalian vertebrate microbiomes in existence. By incorporating emergent next generation sequencing technologies and combining cross-disciplinary methods from the fields of phylogenetics and community ecology, I show that the core reptile gut microbiome is comprised of members of the Proteobacteria, Firmicutes and Bacteroidetes; and that reptile gut bacterial communities are more similar to those of birds than mammals—a previously untested hypothesis. I show that the reptile gut microbiome is strongly influenced by host phylogeny and several ecological traits including parity and foraging mode. My analyses reveal that the composition of the reptile gut microbiome is influenced by who (phylogeny), where (geographic locality) a host organism is and how she lives. Broadly, this work reflects that the microbiome of reptiles is both a phylogenetic and ecological trait that is influenced by selection and that host-associated microbiomes harbor a wealth of natural history information waiting to be explored

The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP)

Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, endoparasites, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date and the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remain unknown. We highlight the potential for the discovery of venom-microbiomes within the adaptive landscape of venom systems. The considerable number of known, convergently evolved venomous animals juxtaposed with the comparatively few studies to identify microbial communities in venom provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics to which we refer to as venom-microbiomics. We also introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing consortium for interested parties to contribute and collaborate within this subdiscipline. Our consortium seeks to support diversity, inclusion and scientific collaboration among all researchers interested in this subdiscipline

Amphibians and reptiles of the Calakmul Biosphere Reserve, México, with new records

We provide a list of amphibians and reptiles of the Calakmul Biosphere Reserve in the southern half of the Mexican Yucatan, in the state of Campeche. The study area was sampled through opportunistic, transect and pitfall trap surveys conducted for three successive years. These surveys resulted in a total of 2,359 amphibian and reptile encounters, belonging to 20 amphibian and 69 reptile species from 24 total families. We present herein the records for one snake, one chelonian and two salamander species not previously recorded in the area

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Data from: The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena)

Ethiopia is a world biodiversity hotspot and harbours levels of biotic endemism unmatched in the Horn of Africa, largely due to topographic—and thus habitat—complexity, which results from a very active geological and climatic history. Among Ethiopian vertebrate fauna, amphibians harbour the highest levels of endemism, making amphibians a compelling system for the exploration of the impacts of Ethiopia's complex abiotic history on biotic diversification. Grass frogs of the genus Ptychadena are notably diverse in Ethiopia, where they have undergone an evolutionary radiation. We used molecular data and expanded taxon sampling to test for cryptic diversity and to explore diversification patterns in both the highland radiation and two widespread lowland Ptychadena. Species delimitation results support the presence of nine highland species and four lowland species in our dataset, and divergence dating suggests that both geologic events and climatic fluctuations played a complex and confounded role in the diversification of Ptychadena in Ethiopia. We rectify the taxonomy of the endemic P. neumanni species complex, elevating one formally synonymized name and describing three novel taxa. Finally, we describe two novel lowland Ptychadena species that occur in Ethiopia and may be more broadly distributed

Snake diets and the deep history hypothesis

The structure of animal communities has long been of interest to ecologists. Two different hypotheses have been proposed to explain origins of ecological differences among species within present-day communities. The competition-predation hypothesis states that species interactions drive the evolution of divergence in resource use and niche characteristics. This hypothesis predicts that ecological traits of coexisting species are independent of phylogeny and result from relatively recent species interactions. The deep history hypothesis suggests that divergences deep in the evolutionary history of organisms resulted in niche preferences that are maintained, for the most part, in species represented in present-day assemblages. Consequently, ecological traits of coexisting species can be predicted based on phylogeny regardless of the community in which individual species presently reside. In the present study, we test the deep history hypothesis along one niche axis, diet, using snakes as our model clade of organisms. Almost 70% of the variation in snake diets is associated with seven major divergences in snake evolutionary history. We discuss these results in the light of relevant morphological, behavioural, and ecological correlates of dietary shifts in snakes. We also discuss the implications of our results with respect to the deep history hypothesis

Sequence_Data

All sequence data collected for this project, named based on the gene

SUPPORTING_RoyalSociety-Rev

The revised supporting information for this publication

A new species of African Snake-Eyed Skink (Scincidae: Panaspis) from Ethiopia

Colston, Timothy J., Pyron, R. Alexander, Bauer, Aaron M. (2020): A new species of African Snake-Eyed Skink (Scincidae: Panaspis) from Ethiopia. Zootaxa 4779 (2): 190-200, DOI: https://doi.org/10.11646/zootaxa.4779.2.

Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs)

Abstract Background The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with statistical and machine learning algorithms to present a phylogenetically informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. Results In contrast to other terrestrial vertebrates and their own diversity in the fossil record, the recent extant lineages of turtles and crocodilians have not experienced any global mass extinctions or lineage-wide shifts in diversification rate or body-size evolution over time. We predict threat statuses for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened turtles and crocodilians in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies. Conclusions Extant turtles and crocodilians maintain unique, conserved morphologies which make them globally recognizable. Many species are threatened due to exploitation and global change. We use taxonomically complete, dated molecular phylogenies and various approaches to produce a comprehensive assessment of threat status and evolutionary distinctiveness of both groups. Neither group exhibits significant overall shifts in diversification rate or body-size evolution, or any signature of global mass extinctions in recent, extant lineages. However, the most evolutionarily distinct species tend to be the most threatened, and species richness and extinction risk are centered in areas of high anthropogenic disturbance, particularly South and Southeast Asia. Range size is the strongest predictor of threat, and a disproportionate amount of evolutionary diversity is at risk of imminent extinction