Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis.

We present a preliminary ND2 phylogeny of South Asian Cnemaspis, recovering a number of deeply divergent clades within Indian Cnemaspis, endemic to the southern and northern Western Ghats besides the Mysore Plateau and hills of Tamil Nadu. There are a number of unnamed lineages that are >5% divergent on ND2 across the phylogeny, including three from the gracilis clade on an elevation gradient (800-1400 m asl.) around Yercaud in the Shevaroy massif, Salem district, Tamil Nadu. We describe two of these as new species- Cnemaspis shevaroyensis sp. nov. and Cnemaspis thackerayi sp. nov. are both allied to Cnemaspis gracilis and can be diagnosed from all other Indian Cnemaspis by the absence of spine-like scales on flank, heterogeneous dorsal pholidosis, presence of femoral and precloacal pores, tail with enlarged, strongly keeled, conical tubercles forming whorls, a median row of enlarged and smooth sub-caudals. They differ from C. gracilis and each other in body size, the number of tubercles around midbody, the number of tubercles in paravertebral rows, the number of femoral and precloacal pores, the number of poreless scales in-between precloacal pores and between femoral and precloacal pores, and subtle colour pattern differences; besides uncorrected mitochondrial sequence divergence (7.9-16.6 %). We also provide a description of Cnemaspis yercaudensis from its type locality and an additional locality. The discovery of two endemic species and a third unnamed divergent lineage from an isolated massif in peninsular India outside the Western Ghats indicate that many other such understudied hill ranges may harbour high endemic biodiversity.

Evolution of ontogenic change in color defenses of swallowtail butterflies.

Natural selection by visually hunting predators has led to the evolution of color defense strategies such as masquerade, crypsis, and aposematism that reduce the risk of predation in prey species. These color defenses are not mutually exclusive, and switches between strategies with ontogenic development are widespread across taxa. However, the evolutionary dynamics of ontogenic color change are poorly understood. Using comparative phylogenetics, we studied the evolution of color defenses in the complex life cycles of swallowtail butterflies (family Papilionidae). We also tested the relative importance of life history traits, chemical and visual backgrounds, and ancestry on the evolution of protective coloration. We found that vulnerable early- and late-instar caterpillars of species that feed on sparsely vegetated, toxic plants were aposematic, whereas species that feed on densely vegetated, nontoxic plants had masquerading and cryptic caterpillars. Masquerading caterpillars resembled bird droppings at early instars and transitioned to crypsis with an increase in body size at late instars. The immobile pupae-safe from motion-detecting, visually hunting predators-retained the ancestral cryptic coloration in all lineages, irrespective of the toxic nature of the host plant. Thus, color defense strategy (masquerade, crypsis, or aposematism) at a particular lifestage in the life cycle of swallowtail butterflies was determined by the interaction between life history traits such as body size and motion levels, phytochemical and visual backgrounds, and ancestry. We show that ontogenic color change in swallowtail butterflies is an adaptive response to age-dependent vulnerability to predation.

Micro-habitat distribution drives patch quality for sub-tropical rocky plateau amphibians in the northern Western Ghats, India.

The importance of patch quality for amphibians is frequently overlooked in distribution models. Here we demonstrate that it is highly important for the persistence of endemic and endangered amphibians found in the threatened and fragile ecosystems that are the rocky plateaus in Western Maharashtra, India. These plateaus are ferricretes of laterite and characterise the northern section of the Western Ghats/Sri Lanka Biodiversity Hotspot, the eighth most important global hotspot and one of the three most threatened by population growth. We present statistically supported habitat associations for endangered and data-deficient Indian amphibians, demonstrating significant relationships between individual species and their microhabitats. Data were collected during early monsoon across two seasons. Twenty-one amphibian taxa were identified from 14 lateritic plateaus between 67 and 1179m above sea level. Twelve of the study taxa had significant associations with microhabitats using a stepwise analysis of the AICc subroutine (distLM, Primer-e, v7). Generalist taxa were associated with increased numbers of microhabitat types. Non-significant associations are reported for the remaining 9 taxa. Microhabitat distribution was spatially structured and driven by climate and human activity. Woody plants were associated with 44% of high-elevation taxa. Of the 8 low-elevation taxa 63% related to water bodies and 60% of those were associated with pools. Rock size and abundance were important for 33% of high elevation specialists. Three of the 4 caecilians were associated with rocks in addition to soil and stream presence. We conclude the plateaus are individualistic patches whose habitat quality is defined by their microhabitats within climatic zones.