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175 results for “ecological divergence”
Data from: Radiating despite a lack of character: ecological divergence among closely related, morphologically similar honeyeaters (Aves: Meliphagidae) co-occurring in arid Australian environments
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Data from: Change in sexual signalling traits outruns morphological divergence across an ecological gradient in the post‐glacial radiation of the songbird genus Junco
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Data from: Genomic and ecological divergence support recognition of a new species of endangered Satyrium butterfly (Lepidoptera, Lycaenidae)
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Neuroanatomical shifts mirror patterns of ecological divergence in three diverse clades of mimetic butterflies
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Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients
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Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex
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Ecological, genetic and geographical divergence explain differences in sunbird (Nectariniidae) colouration
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Supplementary data for Cariou et al (2020, Molecular Ecology Resources, "How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?")
<p>This dataset accompanies a paper by Cariou et al, to be published in Molecular Ecology Resources, where we assessed in 92 insect species if the genetic clustering of specimens into species like units, on the basis of mitochondrial DNA, was consistent with genome wide divergence, as estimated by RAD-seq data. The present repository includes: (1) a detailed description of the bioinformatic analysis indicating which programs were used, together with parameter values, (2) the raw RAD-seq data following demultiplexing, (3) the consensus sequences of all RAD loci for all specimens, and (4) large tables indicating genetic distances at all RAD loci for all species.</p>
Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
Data from: The ecological stage changes benefits of mate choice and drives preference divergence
<p>Preference divergence is thought to contribute to reproductive isolation. Ecology can alter the way selection acts on female preferences, making them most likely to diverge when ecological conditions vary among populations. We present a novel mechanism for ecologically dependent sexual selection, termed 'the ecological stage' to highlight its ecological dependence. Our hypothesized mechanism emphasizes that males and females interact over mating in a specific ecological context, and different ecological conditions change the costs and benefits of mating interactions, selecting for different preferences in distinct environments and different male traits, especially when traits are condition dependent. We test key predictions of this mechanism in a sympatric threespine stickleback species pair. We used a maternal half-sib split-clutch design for both species, mating females to attractive and unattractive males, and raising progeny on alternate diets that mimic the specialized diets of the species in nature. We estimated the benefits of mate choice for an indicator trait (male nuptial color) by measuring many fitness components across the lifetimes of both sons and daughters from these crosses. We analyzed fitness data using a combination of aster and mixed models. We found that many benefits of mating with high color males depended on both species and diet. These results support the ecological stage hypothesis for stickleback. Finally, we discuss the potential role of this mechanism for other taxa and highlight its ability to enhance reproductive isolation as speciation proceeds, thus facilitating the evolution of strong reproductive isolation.</p>
Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)
<p>Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers to gene flow. These studies may conclude absence of population structure, lineage structure that indicates unique species have been discovered, or suggest more research is needed prior to delimitation. Comparative risks of delimiting species incorrectly or failing to delimit species are usually not weighed and a more detailed return to these problems with more data often does not occur. With genomic data and better modeling capabilities we can more clearly delimit species by understanding causes of speciation with respect to biogeography and migration between lineages, the location of hybrid zones in relationship to the ecology of parental lineages, and differential introgression of genes between taxa. Here we examine the origins of three Nearctic milksnakes (<i>Lampropeltis elapsoides, L. triangulum, </i>and <i>L. gentilis</i>) using genomic-scale data to better understand the diversification of these taxa previously delimited based on a smaller genetic dataset. Methods that reject pure isolation by distance in favor of environmentally driven reduction in gene flow clearly indicate that all three lineages should continue to be recognized as unique species. These results underscore conspicuous environmental changes that occur between the sister-taxa forming due to changes in habitat from the Great Plains (GP) to the forested regions of the Eastern Nearctic (ENA). This area has been recognized for turnover of reptile and amphibian species but with few phylogeographic studies examining environmental-genetic structure in this region. We show that the two species meeting at the GP/ENA, <i>L. triangulum </i>and <i>L. gentilis</i>, likely formed in the mid-Pleistocene and have maintained partial reproductive isolation over much of this time, exchanging fewer than one migrant/generation, and formed a hybrid zone with differential introgression of loci. We also show that when <i>L. triangulum</i> and <i>L. gentilis</i> are each in contact with the much older <i>L. elapsoides</i>, some limited gene flow has occurred. We conclude that phylogenetic reticulation in this genus, and likely for many other taxa, is common across throughout time. Furthermore, the application of the biological species concept to the whole genome will give rise to grave misunderstandings of the complexities of how species form and remain unique even in the face of gene flow.</p>
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
<p><span>Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of <i>Streptococcus suis</i>, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of <i>S. suis</i>). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.</span></p>
Data from: Behavioral adaptations imply a direct link between ecological specialization and reproductive isolation in a sympatrically diverging ground beetle
Adaptation to a previously unoccupied niche within a single population is one of the most contentious topics in evolutionary biology as it assumes the simultaneous evolution of ecologically selected and preference traits. Here, we demonstrate behavioral adaptation to contrasting hydrological regimes in a sympatric mosaic of Pogonus chalceus beetle populations, and argue that this adaptation may result in nonrandom gene flow. When exposed to experimental inundations, individuals from tidal marshes, which are naturally subjected to frequent but short floods, showed a higher propensity to remain submerged compared to individuals from seasonal marshes that are inundated for several months. This adaptive behavior is expected to decrease the probability that individuals will settle in the alternative habitat, resulting in spatial sorting and reproductive isolation of both ecotypes. Additionally, we show that this difference in behavior is induced by the environmental conditions experienced by the beetles during their nondispersive larval stages. Hence, accidental or forced ovipositioning in the alternative habitat may induce both an increased performance and preference to the natal habitat type. Such plastic traits could play an important role in the most incipient stages of divergence with gene flow.
Data from: On the causes of rapid diversification in the Páramos: Isolation by ecology and genomic divergence in Espeletia
How diversity arises and what is the relative role of allopatric and ecological divergence are among the most persistent questions in evolution and ecology. Here, we assessed whether ecological divergence has enhanced the diversification of the Neotropical alpine plant complex Espeletia, also known as frailejones. This genus has one of the highest diversification rates ever reported and is distributed in the world's fastest evolving biodiversity hotspot, the Páramo (Neotropical alpine grasslands at elevations of c. 2800–4700 m). Our goal was to determine whether ecology plays a role in divergence within the Espeletia complex by quantifying genome-wide patterns of ecological divergence. We characterized 162 samples of the three most common and contrasting ecotypes (distinct morphotypes occupying particular habitats) co-occurring in six localities in the northern Andes using Genotyping by Sequencing. Contrasting ecotypes were caulescent cloud forest populations, caulescent populations from wind-sheltered and well-irrigated depressions and acaulescent populations from wind-exposed drier slopes. We found high polymorphism with a total of 1,273 single nucleotide polymorphisms (SNPs) that defined the relationships among nine genetic clusters. We quantified allelic associations of these markers with localities and habitats using 18 different general and mixed-effects statistical models that accounted for phylogenetic distance. Despite that these models always yielded more SNPs associated with the localities, markers associated with the habitat types were recovered too. We found strong evidence for isolation-by-distance (IBD) across populations despite rampant gene flow, as expected for plant groups with limited seed dispersal. Contrasts between populations of different habitat types showed that an isolation-by-environment (IBE) trend emerged and masked the IBD signal. Maximum likelihood estimation of the number of migrants per generation (Nem) among ecotypes confirmed the IBE pattern. This result illustrates the importance of mountains' environmental variation at a local scale in generating rapid morphological radiations and maintaining multiple adaptations in a fast-evolving ecosystem like the Páramo.
Data from: Ecological selection as the cause and sexual differentiation as the consequence of species divergence?
Key conceptual issues about speciation go unanswered without consideration of non-mutually exclusive factors. With tests based on speciation theory, we exploit the island distribution and habitat differences exhibited by the Caribbean cricket Amphiacusta sanctaecrucis, and with an analysis of divergent ecological selection, sexually selected differentiation, and geographic isolation, address how these different factors interact. After testing for divergent selection by comparing neutral genetic and morphological divergence in one ecological (mandible shape) and one sexual (male genitalia shape) trait, we examine whether ecological or sexual selection is the primary mechanism driving population divergence. We find that while all three factors—isolation, ecological, and sexual selection—contribute to divergence, and that their interaction determines the stage of completeness achieved during the speciation process, as measured by patterns of genetic differentiation. Moreover, despite the striking diversity in genitalic shapes across the genus Amphiacusta which suggests that sexual selection drives speciation, the significant differences in genitalia shape between forest habitats revealed here implies that ecological divergence may be the primary axis of divergence. Our work highlights critical unstudied aspects in speciation – differentiating the cause from the consequence of divergence—and suggests avenues for further disentangling the roles of natural and sexual selection in driving divergence in Amphiacusta.
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: Ten cases of divergence in the seedling ecology of Dudleya (Crassulaceae)
Dudleya is a genus of succulents consisting of 49 terminal taxa. Many are restricted to narrow geographic ranges with closely related forms living in differing climates. Previously, we found an intriguing set of correlations among nine more or less sympatric Dudleya: species with a smaller mature body size had a lower tolerance for an arid inland climate compared to larger bodied species. Thus, we were motivated to test for rules caused by convergent evolution. We sampled 20 populations from locations across much of the range of the genus. The 20 populations were placed into 10 pairs of close relatives. For each pair, one form was judged to be more mesophilic and the other to be more xerophilic, based on climate-of-origin. We measured germination rate, survival through the summer drought in a coastal garden, and survival through the summer in an inland garden. We hypothesized (among other things) that the xerophilic taxa would have larger mature body sizes and greater rates of survival than mesophilic relatives; however, this and other expected patterns were not repeated across the 10 pairs. Members of pairs have diverged both in various morphological traits and in seedling ecology, but evolution has seemingly not converged on rules. For nearly all taxa, habitat dependence was clear, i.e. plants survived significantly better through the summer at the coastal garden than at the inland garden. Quite possibly the correlations we previously found were caused by divergence between particular lineages coupled with phylogenetic conservatism. Considering the 10 pairs, Dudleya divergences appear to each evolve individualistically.
Data from: Morphological, molecular, and ecological divergence in Pinus douglasiana and P. maximinoi
Pinus douglasiana and P. maximinoi (Pinus subsection Ponderosae) are closely-related New World pines with vague taxonomic boundaries where their natural ranges overlap in western Mexico. They are distinguished from each other by the width of their leaves and thickness of their cone scale apophyses. They are also sometimes confused with two other close relatives, Pinus pseudostrobus and P. yecorensis. We integrated morphological, molecular, and ecological data to clarify the taxonomic limits among these four species. Following previous studies, we evaluated 16 quantitative leaf and seed cone characters. Pinus douglasiana, P. maximinoi, and P. pseudostrobus formed non-discrete groups in multivariate space. The absence of leaf hypodermal intrusions, a persistent peduncle, and the shape of the seed cone are useful for differentiating P. pseudostrobus and P. yecorensis from P. douglasiana or P. maximinoi, and the latter two can usually be distinguished by needle width or cone scale apophysis thickness. Most individuals identified as P. douglasiana, and P. maximinoi shared haplotypes for a plastid ycf1 fragment that is relatively variable for the genus, while P. yecorensis has a closely related, exclusive haplotype. A distinct haplogroup included all individuals of P. pseudostrobus and the remaining individuals of P. douglasiana and P. maximinoi. Leaf width and cone scale thickness of P. douglasiana and P. maximinoi are correlated with elevation. According to potential distribution models, P. yecorensis is distributed in drier areas than P. douglasiana or P. maximinoi, while P. pseudostrobus occurs in more temperate areas, commonly at higher elevations. Pinus douglasiana and P. maximinoi can be considered as incipient species undergoing divergent evolution characterized by incomplete morphological, molecular, and ecological divergence.
Data from: The effect of range overlap on ecological niche divergence depends on spatial scale in monkeyflowers
Patterns of niche divergence and geographical range overlap of closely related species provide insights into the evolutionary dynamics of ecological niches. When ranges overlap, shared selective pressures may preserve niche similarity along coarse‐scale macrohabitat axes (e.g., bioclimates). Alternatively, competitive interactions may drive greater divergence along local‐scale microhabitat axes (e.g., micro‐topographical features). We tested these hypotheses in 16 species pairs of western North American monkeyflowers (Erythranthe and Diplacus, formerly Mimulus) with species' niches, geographic ranges and a robust phylogeny. We found that macrohabitat niche divergence decreased with increasing range overlap, consistent with convergent selection operating at a coarse scale. No significant relationship was detected for microhabitat niches. Additionally, niche divergence was greater for young pairs along all macrohabitat niche axes, but greater for old pairs along one microhabitat axis related to vegetation cover. For a subset of species pairs with partially overlapping ranges, greater microhabitat divergence was detected in sympatry than in allopatry for at least one niche axis for three pairs, consistent with character displacement in sympatry. Thus, coarse‐ and local‐scale niche divergence show dissimilar patterns in relation to range overlap and evolutionary time, perhaps because the relative importance of convergent versus divergent selection depends on spatial scale.
Data from: The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae)
Ecological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (F(ST)), but not absolute (d(XY)), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to 'cold-spots' of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities.
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Allen Brain Atlas
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ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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