The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.

Circadian rhythm and surface activity in soil-dwelling caecilians (Amphibia: Gymnophiona).

The degree to which burrowing, soil-dwelling caecilian amphibians spend time on the surface is little studied, and circadian rhythm has not been investigated in multiple species of this order or by manipulating light-dark cycles. We studied surface-activity rhythm of the Indian caecilians Ichthyophis cf. longicephalus and Uraeotyphlus cf. oxyurus (Ichthyophiidae) and Gegeneophis tejaswini (Grandisoniidae), under LD, DD and DL cycles. We examined daily surface activity and the role of light-dark cycles as a zeitgeber. All three species were strictly nocturnal and G. tejaswini displayed the least surface activity. Four out of thirteen individuals, two I. cf. longicephalus, one G. tejaswini and one U. cf. oxyurus, displayed a more or less distinct surface-activity rhythm in all three cycles, and for the nine other animals the activity patterns were not evident. An approximately 24 h free-run period was observed in the three species. When the light-dark cycle was inverted, surface activity in the three species shifted to the dark phase. The findings of this study suggest that caecilians have a weak circadian surface-activity rhythm, and that the absence of light can act as a prominent zeitgeber in these burrowing, limbless amphibians.

A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source.

Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.

Two extremely rare new species of fossorial salamanders of the genus Oedipina (Plethodontidae) from northwestern Ecuador.

We describe two new species of salamanders of the genus Oedipina, subgenus Oedopinola, from two localities on the northwestern foothills of Ecuador, at elevations between 921 and 1,067 m. These are the southernmost members of the genus. We examined different museum collections and we found just three specimens of Oedipina from Ecuador, obtained throughout the history of herpetological collections in the country. We identify two of the three specimens as new species, but refrain from assigning a specific identity to the third, pending further study. Oedipina villamizariorum sp. n. is a medium-sized member of the genus, with a narrow, relatively pointed head and blunt snout; dorsolaterally oriented eyes, moderate in size; and digits that are moderately long and having pointed tips. Oedipina ecuatoriana sp. n., somewhat larger, has a narrow head and broadly rounded snout; this new species differs from all known Oedipina by the distinctive presence of paired prefrontal bones and a reduced phalangeal formula: 0-0-1-0; 0-1-2-1-1. We provide detailed descriptions of the osteology of both new species. Finally, we present a phylogenetic hypothesis for the genus, including one of the two new species, based on partial sequences of mitochondrial DNA.

Light and electron microscopic observations on the organization of skin and associated glands of two caecilian amphibians from Western Ghats of India.

We adopted light and electron microscopy to understand the structure of the skin of two species of caecilians, Ichthyophis tricolor and Uraeotyphlus cf. oxyurus, from Western Ghats of Kerala, India. The surface of the skin of these caecilians contains an irregular pattern of microridges. Oval, round and polymorphic glandular openings are randomly distributed all over the skin surface. Most of the openings are funnel shaped. The epithelial cells along the rim of the opening descend into the tunnel of the duct. A few glandular openings protrude slightly above the epithelium of the duct. The skin is formed of epidermis and dermis. Small flat disk-like dermal scales, composed of a basal plate of several layers of unmineralized collagen fibers topped with a discontinuous layer of mineralized globular squamulae, are lodged in pouches in the transverse ridges of the skin. Each pouch contains 1-4 scales, which might differ in size. The scales are almost similar between species, yet the difference can be useful in distinguishing between the two species. Flask cells and Merkel cells are present in the epidermis. Two types of glands, mucous and granular, are present in the dermis. The mucous glands are densely packed with mucous vesicles. Darkly stained mucous producing cells are located around the periphery of the gland. Secretory mucous vesicles differ in their organization and distribution. The granular glands are located perpendicular to the skin surface. The granule producing cells of the gland are located near the periphery. There are differently stained spherical secretory granules of various sizes in the cytoplasm. Thus, the use of different microscopic techniques contributed fascinatingly to the first ever understanding of organization of the skin of two selected caecilian species from Western Ghats, revealing certain features to differ between them.

A new species of Indian caecilian highlights challenges for species delimitation within Gegeneophis Peters, 1879 (Amphibia: Gymnophiona: Indotyphlidae).

A new species of indotyphlid caecilian amphibian, Gegeneophis tejaswini sp. nov., is described based on eight specimens from lowlands of the most northerly district of the state of Kerala in the southern part of the Western Ghats region, India. This species is distinguished from all other Gegeneophis in annulation characters and genetics (> 6% different from most similar nominal species for 883 base pairs of mitochondrial 12S and 16S rRNA gene sequence data). The high degree of morphological similarity of G. krishni, G. mhadeiensis and the new species underlines that, for some Gegeneophis, larger samples and/or new characters will be needed to further advance the taxonomy of this genus.

Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India.

Together, Indian plus Seychelles caeciliid caecilian amphibians (Gymnophiona) constitute approximately 10% of the extant species of this order. A molecular phylogenetic analysis of all but one (or two) nominal species (16, in five genera) is presented based on mitochondrial (12S, 16S, cytb, cox1) and nuclear (RAG1) sequence data. Results strongly support monophyly of both Seychelles and peninsular Indian caeciliids, and their sister-group status. Within the Indian caeciliids, Indotyphlus and Gegeneophis are monophyletic sister genera. The phylogenetic position of Gegeneophis ramaswamii, Gegeneophis seshachari, and Gegeneophis carnosus are not well resolved, but all lie outside a well-supported clade of most northern Western Ghats Gegeneophis (madhavai, mhadeiensis, goaensis, danieli/nadkarnii). Most nominal species of Indian caeciliid are diagnosed by robust haplotype clades, though the systematics of G. carnosus-like forms in northern Kerala and southern Karnataka requires substantial further investigation. For the most part, Indian caeciliid species comprise narrowly distributed, allopatric taxa with low genetic diversity. Much greater geographic genetic diversity exists among populations referred to G. seshachari, such that some populations likely represent undescribed species. This, the first phylogenetic analysis of Indian caeciliids, generally provides additional support for recent increases in described species (eight since 1999), and a framework for ongoing taxonomic revision.