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562 results for “genetic divergences”
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: Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the south-western Atlantic and the other along the north-eastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations where found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intra-population genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
Data from: Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback
Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.
Data from: Phenotypic and genetic divergence among harbour porpoise populations associated with habitat regions in the North Sea and adjacent seas.
Determining the mechanisms that generate population structure is essential to the understanding of speciation and the evolution of biodiversity. Here, we investigate a geographic range that transects two habitat gradients, the North Sea to North Atlantic transition, and the temperate to sub-polar regions. We studied the harbour porpoise (Phocoena phocoena), a small odontocete inhabiting both sub-polar and temperate waters. To assess differentiation among putative populations we measured morphological variation at cranial traits (N=462 individuals) and variation at eight microsatellite loci for 338 of the same individuals from Norwegian, British and Danish waters. Significant morphological differentiation reflected the size of the buccal cavity. Porpoises forage in relatively shallow waters preying mainly on benthic species in British and Danish waters, and on mesopelagic and pelagic fish off the coast of Norway. We suggest that the observed differentiation may be explained by resource specialization and either adaptation or developmental responses to different local habitats.
Repeated genetic and adaptive phenotypic divergence across tidal elevation in a foundation plant species
Microgeographic genetic divergence can create fine-scale trait variation. When such divergence occurs within foundation species, then it might impact community structure and ecosystem function, and cause other cascading ecological effects. We tested for parallel microgeographic trait and genetic divergence in Spartina alterniflora , a foundation species that dominates salt marshes of the US Atlantic and Gulf coasts. Spartina is characterized by tall-form (1-2m) plants at lower tidal elevations and short-form (<0.5m) plants at higher tidal elevations, yet whether this trait variation reflects plastic and/or genetically differentiated responses to these environmental conditions remains unclear. In the greenhouse, seedlings raised from tall-form plants grew taller than those from short-form plants, indicating a heritable difference in height. When we reciprocally transplanted seedlings back into the field for a growing season, composite fitness (survivorship and seed production) and key plant traits (plant height and biomass allocation) differed interactively across origin and transplant zones in a manner indicative of local adaptation. Further, a survey of single nucleotide polymorphisms revealed repeated, independent genetic differentiation between tall- and short-form Spartina at 5 of 6 tested marshes across the native range. The observed parallel, microgeographic genetic differentiation in Spartina likely underpins marsh health and functioning, and provides an underappreciated mechanism that might increase capacity of marshes to adapt to rising sea levels.
Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species
Background and Aims: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods: Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion: Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.
Data from: Genetic relationships and ecological divergence in Salix species and populations in Taiwan
Linking ecology with evolutionary biology is important to understand how environments drive population and species divergence. Phenotypically diverse Salix species, such as lowland riparian willow trees and middle- to high-elevation multistemmed shrubs and alpine dwarf shrubs, provide opportunities for studying genetic divergence driven by ecological factors. We used amplified fragment length polymorphism (AFLP) to quantify the genetic variation of 185 individuals from nine populations of four Salix species in Taiwan. Our phylogenetic analyses distinguished two riparian species and the separation of riparian species from multistemmed and dwarf shrub species. Variance partitioning for the total data found that environment explained a substantially larger proportion of genetic variation than geography. However, no genetic variation was explained by geography alone when only compared within and between species. Spatially structured regional environmental effects explained more variation than pure environments in most comparisons within and between species, suggesting that unmeasured environmental variables and/or past demographic histories played important roles in shaping population and species divergence. Based on forward selection analysis, annual mean temperature, aspect, and fraction of absorbed photosynthetically active radiation were the most influential ecological factors in shaping genetic variation within and between species. Nevertheless, different combinations of environmental variables correlated significantly with genetic variation within and between species. We identified eight AFLP loci that potentially evolved under selection intraspecifically using different outlier detection methods. These loci correlated with more than one environmental variable, suggesting local adaptation along environmental gradients at the population level.
Data from: Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican "Lagartijo Jardinero de la Montaña"
Two factors that can lead to geographic structuring in conspecific populations are barriers to dispersal and climatic stability. Populations that occur in different physiographic regions may be restricted to those areas by physical and/or ecological barriers, which may facilitate the formation of phylogeographic clades. Long-term climatic stability can also promote genetic diversification, because new clades are likely to evolve in areas that experience lesser climatic shifts. We conducted a phylogeographic study of the Puerto Rican lizard Anolis krugi to assess whether populations of this anole show genetic discontinuities across the species' range, and if they do, whether these breaks coincide with the boundaries of the five physiographic regions of Puerto Rico. We also assessed whether interpopulation genetic distances in A. krugi are positively correlated with relative climatic stability in the island. Anolis krugi exhibits genetic structuring, but the phylogroups do not correspond to the physiographic regions of Puerto Rico. We used climatic reconstructions of two environmental extremes of the Quaternary period, the present conditions and those during the last glacial maximum, to quantify the degree of climatic stability between sampling locations. We documented positive correlations between genetic distances and relative climatic stability, although these associations were not significant when corrected for autocorrelation. The approach that we employed to assess the relationship between climatic stability and the genetic architecture of A. krugi can also be used to investigate the impact of factors such as the spatial distribution of food sources, parasites, predators or competitors on the genetic landscape of a species.
Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Data from: Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature-associated plastic recombination
Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. The frequency of recombination in the model system Drosophila melanogaster has long been known to exhibit phenotypic plasticity in response to temperature. Here were use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate in response to temperature. In contrast to expectation, we find no evidence for enhanced plasticity in recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct.
Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na+/H+ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.
Data from: Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies
Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species' range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America. Cinnamon Teal showed strong divergence in body size (PC1; PST = 0.56) and exhibited significant frequency differences in a single non-synonymous α-hemoglobin amino acid polymorphism (Asn/Ser-α9; FST = 0.60) between environmental extremes, despite considerable admixture of mtDNA and intron loci (FST = 0.004–0.168). Inferences of strong population segregation were further supported by the observation of few mismatched individuals in either environmental extreme. Coalescent analyses indicated that the highlands were most likely colonized from lowland regions but following divergence, gene flow has been asymmetric from the highlands into the lowlands. Multiple selection pressures associated with high altitude habitats, including cold and hypoxia, have likely shaped morphological and genetic divergence within South American cinnamon teal populations.
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