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FIGURE 5 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 5. Phylogenetic reconstruction of Ahaetulla species revealing the cladistic relationships and lineage diversity. Gray bar depicts species-level entities, some of which are numbered and depicted adjacent to their cluster.

FIGURE 4 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 4. Maps showing the distribution of lineages in the Western Ghats (in Peninsular India) and Sri Lanka. (A) Map showing our study's point locations of Ahaetulla farnsworthi sp. nov., A. isabellina comb. nov., A. malabarica sp. nov., A. borealis sp. nov., A. nasuta & A. oxyrhyncha comb. nov.. (B) Map showing our study's point locations of Ahaetulla perroteti, A. dispar & A. travancorica sp. nov..

FIGURE 13 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 13. Images of Ahaetulla isabellina comb. nov. Images of holotype BNHS 3584 (CESS183). (a) Head lateral, (b) Head Dorsal, (c) Ventral section, (d–f) Dissected hemipenis, (g) Whole specimen. Images of live individuals, (h) BNHS 3584 (CESS183) head lateral, (i) head lateral of CESS182, (j) body section of CESS182. Image of a live, uncollected individual from Valparai, (k) showing threat display (Images a & b; d, e & f to scale, other images not to scale).

FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a number of new lineages (L1–L13) identified in our study. The lineages are marked with grey bars which represent the criteria used to delimit species boundaries, where three gene bPTP (P3), genetic p-distance (GD), morphological separation (M) and geographic isolation (G) are used to predict the number of putative lineages. The nodes below 70% parametric bootstrap support are indicated with asterisk (*). "+" indicates that the status of A. nasuta cf. isabellina needs further work (see Deepak et al. 2019).

FIGURE 16 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 16. Habitat of Ahaetulla malabarica sp. nov. in Brahmagiri Hills, Central Western Ghats (borders Kodagu district, Karnataka State and Waynad district, Kerala State, India) showing semi-evergreen and evergreen forest vegetation types.

FIGURE 9 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 9. Reproductions of colour plates of (a) Coluber nasutus (La Nasique) from Lacepede (1789: 302, pl. 4); (b) Dryinus oxyrhynchus (Passeriki Pam) from Russell (1796: pl. 12); (c) Dryinus russellianus (Botla Passeriki) from Russell (1796: pl. 13); (d) Photo of the preserved skin of BMNH 1904.7.27.25 Dryophis passeriki Photo: Gernot Vogel.

FIGURE 8 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 8. Images of live uncollected Ahaetulla nasuta from Kandy, Sri Lanka (a) Head dorsal, (b) Head lateral, (c) body lateral, (d) body ventrolateral, (e) entire dorsal, (f) [inset] ventral view of specimen with brownish venter.

FIGURE 7 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 7. Images of BNHS 1987 Ahaetulla nasuta. (a) Head lateral. (b) Head dorsal. (c) Ventral. Images of a live, uncollected individual from Sri Lanka A. nasuta. (d) Head lateral. (e) Head dorsal. (f) Ventral (Images a & b to scale, other images not to scale).

FIGURE 2 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 2. PCA plot shows quantitative morphological space shared by Ahaetulla spp.. In the figure, members of the Ahaetulla nasuta species complex with lineages L3—A. borealis sp. nov. (dark blue crosses), L4—A. farnsworthi sp. nov. (green filled squares), L5—A. isabellina comb. nov. (indigo cross) and L6—A. malabarica sp. nov. (blue squares) from the Western Ghats are clustered together and share morphological space with the arid area populations L1—A. oxyrhyncha comb. nov. (circle), L7—A. sahyadrensis nom. nov. and A. anomala (indicated by a black dot). The PCA plots correspond to the scores and loadings presented in Appendix IV (A, B & C)

FIGURE 11 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 11. Images of Ahaetulla sahyadrensis nom. nov. Images of BNHS2015. (a) Head dorsal. (b) Head lateral. (c) Section of body and ventrals. (d–f) Everted Hemipenis. (g) Full specimen. Images of live, uncollected individuals, (h) Near Jog falls, Karnataka, (i) from Agumbe, (j) Kudhremukh, (k) from Agumbe (Images a & b; d, e & f to scale, other images not to scale).

FIGURE 12 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India

FIGURE 12. Images of Ahaetulla pulverulenta, Sri Lanka. (a) Head dorsal, (b) Head lateral, (c) Whole animal (images not to scale).

Data from: Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in adjacent Mountains of Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and USA to hindcast the potential range of Larix laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of broadest areas of past climate suitability for Larix laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of Larix laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM, suggest that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.

Towards genetic modification of plant-parasitic nematodes: Delivery of macromolecules to male germlines and expression of exogenous mRNA in second stage juveniles

Plant-parasitic nematodes are a current and future threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics. Forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate progress in plant-parasitic nematology, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic "tool kit" in plant-parasitic nematodes. We characterise the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, and, taken together, will expedite the development of genetic modification protocols for sedentary endoparasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.

Genomic architecture of a genetically assimilated seasonal color pattern

Developmental plasticity allows genomes to encode multiple distinct phenotypes that can be differentially manifested in response to environmental cues. Alternative plastic phenotypes can be selected through a process called genetic assimilation; although the mechanisms are still poorly understood. We assimilated a seasonal wing color phenotype in a naturally plastic population of butterflies, and characterized three responsible genes. Combined with endocrine assays, and chromatin accessibility and conformation analyses, we found that the transition of wing coloration from an environmentally determined trait to a predominantly genetic trait occurred through selection for regulatory alleles of downstream wing patterning genes. This mode of genetic evolution is likely favored by selection because it allows tissue- and trait-specific tuning of reaction norms without affecting core cue detection or transduction mechanisms.

SUPPLEMENTARY TABLE 3 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

SUPPLEMENTARY TABLE 3. Call properties measurements of Minervarya species A and Minervarya species B in the present study.

SUPPLEMENTARY TABLE 2 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

SUPPLEMENTARY TABLE 2. Morphometric data (in mm) of type specimens of Minervarya caperata deposited at BNHS and described by Kuramoto et al. (2007).

SUPPLEMENTARY TABLE 1 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)

SUPPLEMENTARY TABLE 1. Morphometric data (in mm) of Minervarya species A (M. syhadrensis) and Minervarya species B (M. agricola / M. granosa) from Pune

Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: effect of null alleles

Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79 and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null alleles frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity, and indicate that null alleles were not the only cause of deviation from HW equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlun effect.