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

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

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

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

Panaspis annettesabinae Colston & Pyron & Bauer 2020, sp. nov.

<i>Panaspis annettesabinae</i> sp. nov. <p>(Figs. 1–2)</p> <p>lsid: http://zoobank.org:XXX</p> <p> <b>Holotype.</b> TJC264 (ZMNH H2019,2176), unsexed adult, 8km SW of Bedele on the Metu-Bedele Road, Buno Bedele zone, Oromia Region, (-8.4032°, 36.3105° elevation 1840m; datum WGS 84; Fig. 3) Ethiopia, 9 February 2013 by Timothy J.Colston.</p> <p> <b>Diagnosis.</b> <i>Panaspis annettesabinae</i> can be distinguished from other members of the genus by the following combination of characters: eye in the “ablepharine” condition; scales in 24 rows at the midbody; adult coloration of light-colored upper labials lacking round black spots; coppery dorsum flecked with black, separated from dark brown or black lateral coloration by a single row of light-colored scales; and a coppery bronze tail.</p> <p> <b>Description of the holotype.</b> Unsexed adult in good condition. Body form (size and shape) and scalation typical for <i>Panaspis</i> (Medina <i>et al.</i> 2016). Relatively slender, cylindrical body with pentadactyl fore- and hind-limbs. Trunk elongate; limbs do not overlap when adpressed. Mass 1.3g. SVL 42.1 mm, tail broken in preserved specimen; approximately 1.5 times body length in life. Head length 7.5 mm, with modestly acuminate snout (HL 139% HW). Other measurements presented in Table 1. Rostral wider than high, and visible from above. Nasals widely separated behind rostral by frontonasal. Frontonasal acuminate anteriorly, wider than long. Nostrils large, set centrally in the nasals and not bordering the postnasal. Prefrontals in contact with one another, and first supraocular, first supraciliary and frontal separated from frontonasal by supranasals (which are in contact). Two loreals, the posterior margins of the largest loreal border preoculars (3), which is wider than high. Frontal length less than the distance between anterior tip of frontal and tip of snout; frontal in contact with prefrontals anteriorly, six supraoculars (three on each side) and frontoparietals. Frontoparietals fused, in contact with the frontal, two supraoculars (one on each side), parietals and interparietal. Interparietal triangular with visible parietal window in center; parietals 2 times larger than frontoparietals and contacting each other at the anterior point of the interparietal. Parietals in contact at posterior of interparietal. Four large, broad nuchals collectively bordered by a total of nine dorsals. Supraoculars four (per side). Supraciliaries six, third widest, first tallest. Pretemporals two. Tympanum visible, approximately one third the height of the eye. Supralabials seven, V-VII being the suboculars. Ablepharine eye. Infralabials five. Postmental bordering five scales (mental, two primary chin-shields, and one infralabial on each side). Ventral scales smooth. MSR 24, SAD 62, SAV 68. Limbs with five digits; scales on soles of hands and feet smooth. Relative length of digits of manus IV=III>II>V>I relative length of digits of pes IV>III>II>I>V. Finger-IV scales 12. Tail long, robust and tapering smoothly in life, tail broken on preserved specimen.</p> <p> <b>Coloration in life.</b> Dorsum coppery brown, distinct from darker brown lateral coloration separated by a lighter (whitish tan) stripe encompassing a single scale row. Coppery dorsal coloration flecked with black, loosely arranged in 3–5 irregular lines which become less distinct posteriorly, each black fleck representing one-quarter to one-half of a dorsal scale. Darker brown lateral coloration irregularly interspersed with whitish and blackish speckles. Limbs uniformly darker chocolate brown, with occasional whitish flecking. Coppery dorsal coloration extends onto head scales, uniformly merging into tan-colored rostral. Blackish streak from nostril to orbit, dividing coppery dorsal coloration from whitish labials. Anterior tail coloration (proximo-anterior) similar to limbs, a continuation of the coppery dorsal coloration darkened to uniform chocolate brown. Posterior portion of tail (approximately the final one-third) lighter, more metallic copper coloration, possibly old regrowth or breeding plumage. Ventral coloration not recorded in life</p> <p> <b>Coloration in preservative.</b> In preservative, entire specimen with uniformly milky coloration suggestive of imminent ecdysis. Limbs and light brown, noticeably lighter than the body. Venter uniformly whitish beige, as are underside of limbs. Remnants of narrow dorsolateral stripe still visible, as are black flecks on the dorsum. Unbroken portion of tail and examination of limbs reveals clusters of melanophores across each light-colored scale. Darker blotches evident on tips of dorsal cephalic scales which are otherwise grey or light brown. Coloration of lateral surfaces similar to life, though clouded and faded due to preservation.</p> <p> <b> Comparison with other Ethiopian <i>Panaspis</i>.</b> As noted above, only two species are currently considered to occur in Ethiopia: <i>P. tancredi</i> (known from a single specimen from the northern part of the country—most likely near the region of Debarik, approximately 550km from the type locality of <i>P. annettesabinae</i> in markedly different habitat), and scattered records in the south-central and western regions previously assigned to <i>P. “ wahlbergi ” s.l.</i> Medina <i>et al.</i> (2016) restricted the nominotypical form to southeastern Africa, and revealed that there are no phylogenetically close congeners of TJC264 (<i>P. annettesabinae),</i> which was the sole member of a long branch in all analyses. In their analyses <i>P. annettesabinae</i> is the sister lineage either to most southern African species or several southeastern lineages, dating at least to the Oligocene ~33Ma. As also noted by Ceríaco <i>et al.</i> (2018), the extreme morphological conservatism and crypsis of these species makes comparison and identification difficult in the absence of molecular data. Thus, appropriate and robustly adequate comparisons are difficult and unclear for <i>P. tancredi</i>.</p> <p> From the only known specimen of <i>P. tancredii</i> (an unsexed animal of unknown reproductive status), <i>P. annettesabinae</i> is distinguished by a larger body size (SVL 42.1mm versus 28), 24 dorsal scale rows at midbody (versus 22), blackish flecking on the dorsum (versus lack thereof), whitish flecking on the lateral surfaces (<i>versus</i> lack thereof), and lack of round black spot on upper and lower labials (<i>versus</i> presence). Largen and Spawls (2010) included photographs of two specimens of <i>P. “ wahlbergi ” s.l.</i> from Ethiopia. Neither of these specimens were indicated to have been collected or deposited in a museum for examination. The first (Fig. 267, p. 408) is an adult or subadult from Debre Zeit (Bishoftu) in the central region, and closely resembles the holotype of <i>P. annettesabinae.</i> The second (Fig. 268, p. 408) is a juvenile from Bedele, near the type locality of <i>P. anettesabinae.</i> This specimen also resembles a juvenile version of the holotype, with darker limbs and lateral coloration and less evident dark flecking dorsally and light flecking laterally. A key difference is that the juvenile specimen has a bright blue tail in contrast to the orange tail of the holotype and the Debre Zeit specimen (the latter appears to be regenerated, while the holotype had its original tail in life), though ontogenetic color-change in skink tails (particularly in breeding males) is relatively common. Finally, a series of specimens from Negele Borena in southern Ethiopia represents another new, highly distinct species based on molecular and morphological data (TJC <i>in prep.</i>), suggesting that many of the remaining central and eastern records may belong to this or other new species.</p> <p> <b>TABLE 1.</b> Measurements (in g or mm) and scale counts of the holotype; abbreviations given in the Materials and Methods and definitions following Ceríaco <i>et al.</i> (2018).</p> <p> <b>Distribution.</b> This species is currently known only from the type locality (Fig. 3). Additional fieldwork will be needed to determine the geographic extent of the species’ range. As noted, a juvenile specimen from near the type locality (Largen and Spawls 2010) likely represents an additional record of this species, while an adult or subadult specimen from Debre Zeit may extend the range into central Ethiopia.</p> <p> <b>Habitat and Natural History notes.</b> The habitat at the type locality is a clearing within moist evergreen montane forest (elevation 1840m) in the Oromia Region of southwestern Ethiopia (Fig. 4). This clearing is likely of man-made origin, although natural “glades” within this forest type are known. The clearing sits alongside a stream that has been diverted for use by the Bedele Brewing company, which granted TJC access to camp on and survey the area. While <i>P. annettesabinae</i> is likely more common in forest openings, the type specimen was found underneath a tarp in basecamp during camp maintenance, and it should be noted that while pitfall traps were utilized in the immediate area for 21 consecutive days no other specimens of <i>Panaspis</i> were collected.</p> <p> <b>Etymology.</b> The specific epithet “ <i>annettesabinae</i> ” honors Annette Sabin of the Sabin family, long-time philanthropic supporters of biodiversity conservation. We propose the English vernacular name “Sabin’s Snake-Eyed Skink.”</p>Published as part of <i>Colston, Timothy J., Pyron, R. Alexander & Bauer, Aaron M., 2020, A new species of African Snake-Eyed Skink (Scincidae: Panaspis) from Ethiopia, pp. 190-200 in Zootaxa 4779 (2)</i> on pages 192-195, DOI: 10.11646/zootaxa.4779.2.2, <a href="http://zenodo.org/record/3833467">http://zenodo.org/record/3833467</a&gt

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

Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake.

Vertebrates are metagenomic organisms in that they are composed not only of their own genes but also those of their associated microbial cells. The majority of these associated microorganisms are found in the gastrointestinal tract (GIT) and presumably assist in processes such as energy and nutrient acquisition. Few studies have investigated the associated gut bacterial communities of non-mammalian vertebrates, and most rely on captive animals and/or fecal samples only. Here we investigate the gut bacterial community composition of a squamate reptile, the cottonmouth snake, Agkistrodon piscivorus through pyrosequencing of the bacterial 16S rRNA gene. We characterize the bacterial communities present in the small intestine, large intestine and cloaca. Many bacterial lineages present have been reported by other vertebrate gut community studies, but we also recovered unexpected bacteria that may be unique to squamate gut communities. Bacterial communities were not phylogenetically clustered according to GIT region, but there were statistically significant differences in community composition between regions. Additionally we demonstrate the utility of using cloacal swabs as a method for sampling snake gut bacterial communities

Bacterial community similarity by region and phylogenetic reconstruction of bacterial communities found in Agkistrodon piscivorus.

<p>Graphical representation of bacterial community similarity in GI regions sampled from <i>Agkistrodon piscivorus</i> individuals: A- C) Venn diagrams of small intestine (A), large intestine (B) and cloacal (C) samples from the three individuals sampled destructively (103, 110, 111). Circles are drawn such that the area of the circle is proportional to the number of OTUs found in each region. Numbers represent the number of OTUs either shared or specific to that individual. D) 95% majority rule consensus tree based on Yue & Clayton theta distances for bacterial communities in all individuals sampled (numbered) with branches colored by sample region (blue = small intestine, black = large intestine, red = cloacal).</p