A three-dimensional genomics view for speciation research.

Genomic information is folded in a three-dimensional (3D) structure, a rarely explored evolutionary driver of speciation. Technological advances now enable the study of 3D genome structures (3DGSs) across the Tree of Life. At the onset of 3D speciation genomics, we discuss the putative roles of 3DGSs in speciation.

Developmental plasticity in amphibian larvae across the world: Investigating the roles of temperature and latitude.

Temperature-induced developmental plasticity could allow amphibian larvae to complete metamorphosis successfully despite new thermal challenges and increased desiccation risk due to climate change. Here we investigated how the capacity for temperature-induced developmental plasticity varies with latitude and whether population-specific biogeographic background accounts for the different degree of plastic responses to temperature. We carried out a combined analysis based on the data from 150 studies (93 articles) performed on 64 amphibian species. We collected empirical data for age and size at metamorphosis in amphibian larvae acclimated to different temperatures during development and found that all larvae from all populations in these studies revealed a change in metamorphic traits with a given change in temperature and thus, were able to exhibit temperature-induced developmental plasticity. Age at metamorphosis was more affected by temperature than size at metamorphosis. Age and size at the onset of metamorphosis were generally lowest at warmest temperatures during development. Furthermore, populations from tropical latitudes were less sensitive to a change in developmental temperature compared to populations from higher latitudes. Accordingly, we suggest tropical populations to be the most vulnerable to increasing temperatures during metamorphosis. Our analyses reveal biases with respect to taxonomy, biogeographic distribution of species, and study design. Data from tropical populations are underrepresented and thus, the capacity for developmental plasticity of the most threatened species probably remains poorly understood. Future studies should focus on under-represented regions, most threatened species, and include a broader range of temperatures during development in order to make robust projections on future sensitivity of populations to climate change.

A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation.

The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.

The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure.

The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name 'North' (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and 'South' (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.

A distinct new species of riparian rock-dwelling gecko (genus: Hemidactylus) from the southern Western Ghats.

We describe a new species of rock-dwelling gecko, Hemidactylus paaragowlipaaragowli sp. nov., from the Agastyamalai Hill Range, in the southern Western Ghats. Morphological and molecular data support the distinctiveness of the species and its close relationship to other large-bodied, tuberculate Hemidactylus spp. from the H. prashadi group from India and Sri Lanka. This species belongs to a rupicolous complex and can be distinguished from other members of the group based on the following characters: 22-24 longitudinal rows of fairly regularly arranged, subtrihedral, weakly keeled, striated tubercles at midbody; 9-11 and 10-12 subdigital lamellae on the first and fourth digits, respectively, of both manus and pes; tail with transverse series of four enlarged tubercles on each tail segment; 10-12 femoral pores on each side separated by 16-18 scales without pores; 11-13 supralabials and 9-10 infralabials.