Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus.

BACKGROUND: Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS: We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS: Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.

Prudent burrow-site selection in a landscape of fear.

Prey should select safer breeding sites over riskier sites of otherwise similar habitats. This preference, however, may differ between conspecifics of different competitive abilities if the costs of intraspecific competition overpower the benefits of breeding in a safer site. Our goal was to test this hypothesis by exploring the burrow-site selection of different-sized desert isopods (Hemilepistus reaumuri) near and away from a scorpion burrow. We found that larger females are more likely to occupy burrows than smaller females, regardless of whether these burrows were close or away from scorpion burrows. We also found that larger females stayed longer in safer burrows and that smaller females tended to stay longer in riskier sites even in the absence of direct competition, implying a prudent burrow-site selection. We found no association between male size and the tendency to occupy or to spend time in a burrow, regardless of whether these burrows were close or away from scorpion burrows. Our work highlights the need to consider intraspecific competition when exploring how predators regulate prey behaviour.

Optimizing ddRAD sequencing for population genomic studies with ddgRADer.

Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.

Two new species of yellow-tailed Hemidactylus Goldfuss, 1820 (Squamata: Gekkonidae) from rocky outcrops on the Telangana Plateau, India.

Two distinct species of the gekkonid genus Hemidactylus are described from the dry zone of peninsular India from the state of Telangana. The two sister species, Hemidactylus flavicaudus sp. nov. and H. xericolus sp. nov., are nested within the morphologically cryptic H. brookii group, but are clearly distinguishable from all known species in having a bright yellow tail and yellow markings on the head, besides unique combinations of meristic characters and small body size (< 45 mm snout to vent length). The two new species are also deeply divergent from each other and other members of the H. brookii group in mitochondrial NADH dehydrogenase 2 and cytochrome b sequences. Hemidactylus flavicaudus sp. nov. can be diagnosed from H. xericolus sp. nov. based on the number of dorsal tubercle rows at midbody (11-14 versus 6-8). These descriptions of evolutionarily and morphologically distinct species highlight the dearth of studies carried out in the dry zone of peninsular India and the urgent need to assess biodiversity in the face of rapid land-use changes in this landscape.

Repeated evolution of terrestrial lineages in a continental lizard radiation.

The "early-burst" model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the "early-burst" hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs-terrestrial and scansorial species-that vary significantly in body size and toepad size were identified. Unlike the prediction of the "early-burst" model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the Ornstein-Ulhenbeck model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19-12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.

Eocene-Oligocene cooling and the diversification of Hemidactylus geckos in Peninsular India.

The Eocene-Oligocene cooling marks a global shift towards a cooler and drier climate, concurrent with significant turnover in biota globally. In Peninsular India, palynological investigations suggest a shift from wet rainforest vegetation to dry and seasonal species during this period. However, the grassland and open habitats that dominate this region at present expanded relatively recently due to Late Miocene intensification of monsoon seasonality. We test the possible role of these climatic shifts in generating the dry habitat diversity of an endemic radiation of Hemidactylus geckos distributed in both wet and dry habitats, by investigating whether (a) the beginning of the diversification of dry habitat lineages overlap with the Eocene-Oligocene cooling or late Miocene aridification and (b) accompanied by an increase in diversification. Molecular data (two nuclear and two mitochondrial gene fragments) were generated for samples collected across Peninsular India, and along with previously published data, a time-calibrated phylogeny was reconstructed. Ancestral state reconstruction of dry and wet habitat states was carried out on the time-calibrated phylogeny and γ-statistics along with a test for diversity-dependent diversification utilized to examine the trend in lineage accumulation. Results show the ancestral node of this radiation to have a dry habitat state, which began diversifying between 39 and 32 million years ago, concurrent with the Eocene-Oligocene cooling. Furthermore, lineage diversification fit a diversity-dependent model of diversification and the γ-statistics revealed an early increase in diversification followed by a slowdown later. The deep divergences of dry habitat lineages concurrent with the Eocene-Oligocene cooling suggest that this could have served as an ecological opportunity facilitating an early increase in lineage diversification of Hemidactylus in this region. These results suggest an ancient origin and long persistence of arid ecosystems in Peninsular India.

A novel member of the Hemidactylus brookii complex (Squamata: Gekkonidae) from the Western Ghats of Maharashtra, India.

A new rupicolous gecko from the Hemidactylus brookii complex is described from the forests and plateaus of Amboli, in the Western Ghats of Maharashtra. This medium sized (average adult SVL 56.2±5.0 to at least 62 mm), nocturnal species is superficially similar to other congeners from the 'H. brookii' clade, but can be distinguished from them in having 17 or 18 fairly regular longitudinal rows of enlarged, conical, keeled tubercles at midbody, extending from posterior part of the head to groin; tubercles in parasagittal rows smaller, feebly keeled and more rounded; approximately six rows of tubercles on either side of parasagittal tubercle rows, highly enlarged, remarkably conical and strongly keeled; lamellae divided in a straight transverse series-seven or eight lamellae beneath fourth digit (manus and pes) and five or six beneath first digit (manus and pes). Males with nine or ten (rarely eight) femoral pores separated by four or five poreless scales; supralabials 11-13; infralabials 8-11. Molecular data based on the mitochondrial ND2 gene supports the distinctiveness of this species and helps ascertain its phylogenetic position within the 'H. brookii' group of the Indian Hemidactylus radiation.

A new cryptic, rupicolous species of Hemidactylus Oken, 1817 (Squamata: Gekkonidae) from Meghamalai, Tamil Nadu, India.

A distinct new gecko of the genus Hemidactylus is described from the Meghamalai massif in Tamil Nadu, India. This large sized (average SVL 88.2±16.0 to at least 112.2 mm), cryptic, rock-dwelling species is superficially similar to its tuberculate South Asian congeners of comparable size, but can be distinguished from them in having 17-19 longitudinal rows of fairly regularly arranged, strongly keeled, striated tubercles with the two most medial parasagittal rows smaller, flatter, strongly keeled and rounded, increasing in size laterally and becoming strongly conical at the flanks; 8-10 and 10-12 sub-digital lamellae under the first and fourth digits respectively of both manus and pes; 17-22 femoral pores on each side separated medially by a diastema of 10-11 poreless scales; 11-15 supralabials and 9-14 infralabials. Molecular data supports the distinctiveness of this species and helps ascertain its phylogenetic position within the larger Indian Hemidactylus clade.

The curious case of Hemidactylus gujaratensis (Squamata: Gekkonidae).

Hemidactylus Oken, 1817 is one of the most speciose genera of the family Gekkonidae with more than 140 described species (Uetz et al. 2016). While this genus naturally occurs across the tropics and subtropics, a substantial part of its distribution also results from human-mediated dispersal. Carranza Arnold (2006) retrieved five broad clades in a global phylogeny of Hemidactylus, one of which has species distributed in tropical Asia. Subsequent work by Bauer et al. (2010) and Bansal Karanth (2010) revealed that the species from tropical Asia fell into two deeply divergent and potentially non-sister sub-clades-one comprising a large radiation confined to peninsular India and Sri Lanka (the Indian radiation, IR), and the other comprising species largely distributed in Southeast (SE) Asia.

A new rock dwelling Hemidactylus (Squamata: Gekkonidae) from Chhattisgarh, India.

A distinct new species of gecko of the genus Hemidactylus is described from the Kanker district of Chhattisgarh State, east-central India. This large-sized (SVL average 81.33±13.40 to at least 98.0 mm) Hemidactylus is characterized by a dorsum with small granules, intermixed with 10-12 rows of irregularly arranged, slightly larger, rounded, weakly-keeled tubercles at midbody; 10-12 and 13-15 subdigital lamellae on the first and fourth digits, respectively, of both manus and pes; a single enlarged postcloacal tubercle on either side of the tail; 10-12 femoral pores on each thigh separated by 5-8 poreless scales; 12-14 supralabials and 10-12 infralabials.