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562 results for “genetic divergences”
Data from: Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish
<p>Recent work has revealed the importance of contemporary evolution for shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically-important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead / resident rainbow trout (<em>Oncorhynchus mykiss</em>). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size-structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident <em>O. mykiss</em> populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.</p>
Song and genetic divergence within a subspecies of white-crowned sparrow (Zonotrichia leucophrys nuttalli)
<p><span>Animal culture evolves alongside </span><span>genomes</span><span>, and</span><span> the two modes of inheritance—culture and genes—interact in myriad ways.</span> <span>For example,</span><span> stable geographic variation </span><span>in culture can act as </span><span>a </span><span>reproductive barrier</span><span>, </span><span>thereby producing genetic divergence</span><span> between "cultural populations</span><span>.</span><span>"</span> <span>White-crowned sparrows (</span><span>Zonotrichia</span> <span>leucophrys</span><span>) are a </span><span>well-established</span><span> model species for bird song</span><span> learning</span><span> and cultural evolution</span><span>, as t</span><span>hey </span><span>have </span><span>distinct</span><span>, </span><span>geographically </span><span>discrete</span><span>, and culturally transmitted</span> <span>song </span><span>types</span><span> (i.e., song dialects)</span><span>. </span><span>In this study, we tested </span><span>the hypothesis that</span> <span>divergence between </span><span>culturally transmitted </span><span>songs </span><span>drive</span><span>s</span> <span>genetic divergence</span> <span>with</span><span>in Nuttall's white-crowned sparrows (</span><span>Z. l. </span><span>nuttalli</span><span>).</span><span> In accordance with sexual selection theory, we hypothesized that cultural divergence between mating signals both preceded and generated genetic divergence.</span><span>We characterized the population structure and song variation in the subspecies and found two </span><span>genetic</span><span>ally differentiated</span> <span>populations </span><span>whose</span><span> boundary</span> <span>coincid</span><span>es</span><span> with a major </span><span>song </span><span>boundary</span><span> at Monterey Bay</span><span>, California</span><span>.</span> <span>We then</span><span> conducted a song playback experiment </span><span>that </span><span>demonstrated males discriminate between songs based on their degree of divergence from the</span><span>ir</span><span> local dialect</span><span>. These results</span> <span>support</span><span> the idea that discrimination against non-local songs</span><span> is driving genetic divergence between the northern and southern populations. </span><span>Altogether, t</span><span>his</span><span> study</span><span> provides evidence that</span><span> cultura</span><span>lly transmitted bird songs can act as the foundation for speciation by sexual selection</span><span>.</span></p>
FIGURE 5 in A new species of Knodus (Characiformes: Characidae), with deep genetic divergence, from the Mearim and Munim river basins, Northeastern Brazil, and evidence for hidden diversity in adjacent river basins
FIGURE 5 | Geographical distribution of Knodus guajajara.
Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation, and elevation) and genetic factors (genetic distance based on RADseq loci) as correlates of population divergence in venom phenotypes. We found that over half of the variation in venom composition is associated with among-population differentiation for genetic and environmental variables, and that this variation occurred along axes defining previously observed functional trade-offs between venom proteins that have neurotoxic, myotoxic and hemorrhagic effects. Surprisingly, genetic differentiation among populations was the best predictor of venom divergence, accounting for 46% of overall variation, whereas differences in prey community composition and abiotic factors explained smaller amounts of variation (23% and 19%, respectively). The association between genetic differentiation and venom composition could be due to an isolation by distance effect or, more likely it may reflect an isolation-by-environment effect where selection against recent migrants is strong, producing a correlation between neutral genetic differentiation and venom differentiation. Our findings suggest that even coarse estimates of prey community composition can be useful in understanding the selection pressures acting on patterns of venom protein expression. Additionally, our results suggest that factors other than adaptation to spatial variation in prey need to be considered when explaining population divergence in venom.
Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations
<p><b>PREMISE </b></p> <p>Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments.</p> <p><b>METHODS </b></p> <p>We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (<i>Mimulus cardinalis</i>).</p> <p><b>RESULTS </b></p> <p>We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats.</p> <p><b>CONCLUSIONS </b></p> <p>Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates. </p>
Figure 6 in Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)
Figure 6. One song strophe of Cettia a. concolor, Taiwan, May; tape recording by Per Alström.
Data from: Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola
<p>Understanding the genetic basis of species differences is a major goal in evolutionary biology. Pigmentation divergence between <i>Drosophila </i>species often involves genetic changes in pigmentation candidate genes that pattern the body and wings, but it remains unclear how these changes affect pigmentation evolution in multiple body parts between the same diverging species. <i>Drosophila elegans </i>and <i>D. gunungcola</i> show pigmentation differences in the thorax, legs, and wings, with <i>D. elegans </i>exhibiting male-specific wing spots and <i>D. gunungcola </i>lacking wing spots with intensely dark thoraces and legs. Here, we performed QTL mapping to identify the genetic architecture of these differences. We find a large effect QTL on the X chromosome for all three body parts. QTL on Muller Element E were found for thorax pigmentation in both backcrosses but were only marginally significant in one backcross for the legs and wings. Consistent with this observation, we isolated the effects of the Muller Element E QTL by introgressing <i>D. gunungcola </i>alleles into a <i>D. elegans </i>genetic background and found that <i>D. gunungcola </i>alleles linked near the pigmentation candidate gene <i>ebony </i>caused intense darkening of the thorax, minimal darkening of legs, and minimal shrinking of wing spots. <i>D. elegans</i> <i>ebony</i> mutants showed changes in pigmentation consistent with Ebony having different effects on pigmentation in different tissues. Our results suggest that multiple genes have evolved differential effects on pigmentation levels in different body regions.</p>
Genetic and ecomorphological divergence between sympatric Astyanax morphs from Central America
<p>Intraspecific ecological and morphological polymorphism can promote ecological speciation and the build-up of reproductive isolation. Here, we evaluate correlations among morphology, trophic ecology, and genetic differentiation between two divergent morphs (<i>elongate</i> and <i>deep-body</i>) of the fish genus <i>Astyanax</i> in the San Juan River basin in Central America, to infer the putative evolutionary mechanism shaping this system. We collected the two morphs from three water bodies and analyzed: 1) the correlation between body shape and the shape of the premaxilla, a relevant trophic morphological structure, 2) the trophic level and niche width of each morph, 3) the correspondence between trophic level and body and premaxillary shape, and 4) the genetic differentiation between morphs using mitochondrial and nuclear markers. We found a strong correlation between the body and premaxillary shape of the morphs. The elongate-body morph had a streamlined body, a premaxilla with acuter angles and a narrower ascending process, and a higher trophic level, characteristic of species with predatorial habits. By contrast, the deep-body morph had a higher body depth, a premaxilla with less acute angles, and a broader trophic niche, suggesting generalist habits. Despite the strong correlation between morphological and ecological divergence, the morphs showed limited genetic differentiation, supporting the idea that morphs may be undergoing incipient ecological speciation, although alternative scenarios such as stable polymorphism or plasticity should also be considered. This study provides support for the role of ecological factors promoting diversification in lake and stream-dwelling freshwater fish.</p>
The oceanographic isolation of the Ogasawara Islands and genetic divergence in a reef-building coral
<p><strong><span>Aim:</span></strong><span> Due to their spatial isolation, oceanic islands are natural systems to study evolutionary divergence. The Ogasawara Islands belong to the most isolated archipelagos on Earth and are well-known for their high terrestrial endemicity, however, less is known about the marine realm. Here, we analyze the degree of oceanographic isolation of the archipelago based on genetic data of a reef-building coral and a biophysical dispersal model.</span></p> <p><strong><span>Location: </span></strong><span>North-Western Pacific (Ogasawara, Ryukyu, Daito Islands, Guam)</span></p> <p><strong><span>Taxon: </span></strong><em><span>Galaxea fascicularis </span></em><span>L.</span></p> <p><strong><span>Method:</span></strong><span> Three to 15 specimens were sampled at several sites in Ogasawara and its closest potential migration sources in southern Japan and the Mariana Islands (Guam) and RAD-sequenced. 108 specimens from the common Pacific lineages 'L' (Ryukyu- and Daito Islands, Guam) and 'Ogasawara' (Ogasawara) were analyzed with population genetics and demographic modeling<em>.</em> Oceanographic dispersal was investigated by inverse particle tracking using a Lagrangian particle advection simulation based on ROMS and applying biological dispersal parameters of <em>G. fascicularis</em>.</span></p> <p><strong><span>Results:</span></strong><span> The <em>G. fascicularis </em>population in Ogasawara is genetically highly differentiated from the next closest reefs in the region and has diverged from the Ryukyu Islands under very little, asymmetric, eastward migration. Inverse particle tracking confirmed the oceanographic isolation of Ogasawara and showed that the islands are rarely but most likely reached by settlers from the Ryukyu Islands by long-distance-dispersal of exceptionally long-lived larvae (>44 days), with no dispersal <em>vice versa</em>. </span></p> <p><strong><span>Main conclusions: </span></strong><span>Ogasawara is a dispersal sink location and t</span><span>he high degree of genetic differentiation in <em>Galaxea </em>has resulted from strong oceanographic isolation.</span> <span>This research highlights how oceanographic features impact species-level genetic differentiation even in well-dispersed taxa such as broadcast-spawning corals, and they are likely even more pronounced in less vagile organisms<em>.</em> These findings suggest the Ogasawaran Archipelago should be considered an important priority for marine conservation, alongside its high importance for terrestrial conservation. </span></p>
Data for: Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback
<p>Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here 'parallel evolution') often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (<em>Gasterosteus aculeatus</em>) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.</p>
Data from: Genetic divergence along a climate gradient shapes chemical plasticity of a foundation tree species to both changing climate and herbivore damage
<p><span>Climate change is threatening the persistence of many tree species via independent and interactive effects on abiotic and biotic conditions. In addition, changes in temperature, precipitation, and insect attacks can alter the traits of these trees, disrupting communities and ecosystems. For foundation species such as <em>Populus</em>, phytochemical traits are key mechanisms linking trees with their environment and are likely jointly determined by interactive effects of genetic divergence and variable environments throughout their geographic range. Using reciprocal Fremont cottonwood (<em>Populus</em> <em>fremontii</em>) common gardens along a steep climatic gradient, we explored how environment (garden climate and simulated herbivore damage) and genetics (tree provenance and genotype) affect both foliar chemical traits and the plasticity of these traits. We found that: 1) Constitutive and plastic chemical responses to changes in garden climate and damage varied among defense compounds, structural compounds and nitrogen. 2) For both defense and structural compounds, plastic responses to garden climate depended on the climate in which a population or genotype evolved. Specifically, trees originating from cool provenances showed higher defense plasticity in response to climate changes than trees from hotter provenances. 3) Trees from cool provenances growing in cool conditions expressed the lowest constitutive defense levels but the strongest induced (plastic) defenses. 4) The combination of hot growing conditions and simulated herbivory switched the strategy used by these genotypes, increasing constitutive defenses but erasing the capacity for induction. Because Fremont cottonwood chemistry plays a major role in shaping riparian communities and ecosystems in the southwestern US, the effects of changes in phytochemical traits can be wide-reaching. As the southwestern US is confronted with warming temperatures and insect outbreaks, these results improve our capacity to predict ecosystem consequences of climate change and inform selection of tree genotypes for conservation and restoration purposes. </span></p>
The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds
<p>Trait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (<em>Leucosticte</em> spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.</p>
Data from: Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)
<p>Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes, <em>Sebastes schlegelii</em> and <em>S. trivittatus</em>, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between two backcross families and two developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage-specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane's rule in terms of hybrid inviability does not hold. Additionally, QTL mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including <em>agouti-signaling protein 1</em> (<em>asip1</em>) and <em>melanocortin 1 receptor</em> (<em>mc1r</em>), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.</p>
Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
<p>We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.</p>
Dataset for: Plasticity and genetic effects contribute to different axes of neural divergence in a community of mimetic Heliconius butterflies
<p>Changes in ecological preference, often driven by spatial and temporal variation in resource distribution, can expose populations to environments with divergent information content. This can lead to adaptive changes in the degree to which individuals invest in sensory systems and downstream processes, to optimize behavioural performance in different contexts. At the same time, environmental conditions can produce plastic responses in nervous system development and maturation, providing an alternative route to integrating neural and ecological variation. Here, we explore how these two processes play out across a community of <em>Heliconius</em> butterflies. <em>Heliconius</em> communities exhibit multiple Mullerian mimicry rings, associated with habitat partitioning across environmental gradients. These environmental differences have previously been linked to heritable divergence in brain morphology in parapatric species pairs. They also exhibit a unique dietary adaptation, known as pollen feeding, that relies heavily on learning foraging routes, or trap-lines, between resources, which implies an important environmental influence on behavioural development. By comparing brain morphology across 133 wild-caught and insectary reared individuals from seven <em>Heliconius</em> species, we find strong evidence for interspecific variation in patterns of neural investment. These largely fall into two distinct patterns of variation; first, we find consistent patterns of divergence in the size of visual brain components across both wild and insectary reared individuals, suggesting genetically encoded divergence in the visual pathway. Second, we find interspecific differences in mushroom body size, a central component of learning and memory systems, but only among wild caught individuals. The lack of this effect in common-garden individuals suggests an extensive role for developmental plasticity in interspecific variation in the wild. Finally, we illustrate the impact of relatively small-scale spatial effects on mushroom body plasticity by performing experiments altering the cage size and structure experienced by individual <em>H. hecale</em>. Our data provide a comprehensive survey of community level variation in brain structure, and demonstrate that genetic effects and developmental plasticity contribute to different axes of interspecific neural variation.</p>
Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
<p><span>Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus <em>Clarkia</em>. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other <em>Clarkia </em>taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa – a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.</span></p>
Dataset for: Plasticity and genetic effects contribute to different axes of neural divergence in a community of mimetic Heliconius butterflies
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Data from: A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific
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Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska
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Data from: Adaptive landscape genetics and malaria across divergent island bird populations
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