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opencc-zeroAug 2020View details →

Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species R. mendax that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and R. mendax show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on R. mendax revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in Rhagoletis. The generality of this result is placed in the context of other similar systems.

opencc-zeroNov 2023View details →

Data for: Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of two species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the two parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. Three vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and five floral traits (corolla length and width, anther insertion, petal color, nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the I. tenuituba site, whereas selection favored the reverse condition at the I. aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

opencc-zeroJan 2024View details →

Data from: Mating environments mediate the evolution of behavioral isolation during ecological speciation

The evolution of behavioral isolation is often the first step towards speciation. While past studies show that behavioral isolation will sometimes evolve as a by-product of divergent ecological selection, we lack a more nuanced understanding of factors that may promote or hamper its evolution. The environment in which mating occurs may be important in mediating whether behavioral isolation evolves for two reasons. Ecological speciation could occur as a direct outcome of different sexual interactions being favored in different mating environments. Alternatively, mating environments may vary in the constraint they impose on traits underlying mating interactions, such that populations evolving in a 'constraining' mating environment would be less likely to evolve behavioral isolation than populations evolving in a less constraining mating environment. In the latter, mating environment is not the direct cause of behavioral isolation but rather permits its evolution only if other drivers are present. We test these ideas with a set of 28 experimental fly populations, each of which evolved under one of two mating environments and one of two larval environments. Counter to the prediction of ecological speciation by mating environment, behavioral isolation was not maximal between populations evolved in different mating environments. Nonetheless, mating environment was an important factor as behavioral isolation evolved among populations from one mating environment but not among populations from the other. Though one mating environment was conducive to the evolution of behavioral isolation, it was not sufficient: assortative mating only evolved between populations adapting to different larval environments within that mating environment, indicating a role for ecological speciation. Intriguingly, the mating environment that promoted behavioral isolation is characterized by less sexual conflict compared to the other mating environment. Our results suggest that mating environments plays a key role in mediating ecological speciation via other axes of divergent selection.

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B. 'bufonivora_EUROPE_A' represents a consistent haplotype present in all 12 samples from Europe (Table 1), of which just two were heterozygous ('bufonivora_frog' and 'bufonivora_NLWi'). 'bufonivora_CAN' and 'elongata_CAN' are represented by two samples each, none of which were heterozygous. Scale bar represents expected changes per site.

Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 2. Bayesian Inference tree constructed from Internal transcribed Spacer 2 (non-coding) sequence data. Each specimen is labelled with the species name and location abbreviation as indicated in Table 1. Green text corresponds to European samples of Lucilia bufonivora; red represents Lucilia elongata; purple represents Canadian L. bufonivora; orange represents Lucilia silvarum. Scale bar represents expected changes per site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. Divergence times estimated from a in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 6. Divergence times estimated from a concatenated data set of per, COX1 and ITS2 sequences for the Lucilia bufornivora species group. Substitution model and relaxed clock models were unlinked for each gene. The tree was calibrated by setting the root to the node age corresponding to the split between Luciilinae and Calliphorinae subfamilies (~19 mya) as estimated by Wallman et al. (2005). Blue bars represent 95% highest posterior density (HPD) of each node age. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 1. Location of samples for which the COX1 gene was sequenced in this study. Boxes represent the locations of individual samples: red, Lucilia elongata; orange, Lucilia silvarum; green, Lucilia bufonivora.

Figure 1 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 1. ContinentalFrancewiththedepartmentMayennehighlighted (A) andhabitatmodelforthe Fire salamander indepartment Mayenne (B). Themap representsthe habitat suitability model Ps = (1/ (1 + exp(−0.0303*percent_forest_cover-0.00562*altitude-0.0299*percent_hedgerow_cover + 1.769))) and was visualized with ILWIS 3.6 software58, available at https://52north.org/software/software-projects/ilwis/. Habitat suitability increases from deep blue with a probability of occurrence of zero to deep red with a probability of occurrence at unity (see colour bar). Prime fire salamander habitats are found at higher altitudes and are forested (in black) or with a dense hedgerow cover. Populations genetically investigated are located in and around the largely deciduous forests Forêt de Bourgon (FB) and Bois de Hermet (BH) and listed in Table 1.The outer geographicalcoordinates of the department are 1.239–0.049W and 47.733–48.568N.

Figure 3 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 3. (A) Clustering of pairwise Fst-values of Kottenforstfire salamanderpopulations (localities K01-K47) with the UPGMA-method. Numbers K01-K27 represent populations in the western section of the forest and K28-K47 represent populationsin the eastern section of the forest. The basal cluster at Fst <0.04 is composed of two groups (shaded) composed of mostly eastern (14/16 = 88%) or mostlywestern localities (14/15 = 93%). Populations breeding in streams are shown by the letter S. Note that populations that join the dendrogram at higher Fst-values are characterized by mostlysmall effectivepopulation sizes (Ňe ≤ 10, indicated by small open dots; X – Ňe not determined). B top panel - Populationsplotted along the firstand second axis of a principal component analysis. Middle panel - Ellipses represent means ± standarddeviation for sevenstream populations (left ellipse) and 40 non-streampopulations (right ellipse). Lower panel - Ellipsesrepresent means ± standard deviation forthe western (left) and eastern (right) sectionof the Kottenforst, forsmall populations (Ňe ≤ 10) shown by interruptedlines andfor larger populations (Ňe> 10) shown by uninterrupted lines. Notethat for the larger populations the ellipses for western and eastern localities do not overlap.

Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 analyzed in the framework of allopatric speciation, i.e. a secondary spatial contact of a western pond-breeding lineage and an eastern stream-breeding lineage. The 95% credible cline regions are shown by grey shading. Solid and open round symbolsrepresent larger (Ňe> 10) andsmall populations (Ňe ≤ 10), respectively. Note that the stream-breeding populations that gave the composite genotype its name are all located in the eastern section of the Kottenforst (six data points indicated with a forward slash (/). One 'intermittent stream' in the western section is indicated by a backward slash. Also note the paucity of data at and around the steepest part of the clines. A – loadings on the first PC axis versus geographical distance. The clinecentre is at km 365.3 of the Universal Transverse Mercator (UTM) grid. Cline width is 3952 m. B – frequency of the stream-breeding genotype versus distance (after21). Thecline centre is at UTM km 365.1 and the cline widthis 1108 m. For model details see Supplementary Information VI.

Figure 2 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 2. (A) Clustering of pairwise Fst-values of firesalamander populations (Mayenne localities 1–41) with the UPGMA-method. The basal cluster at Fst <0.010 is mostly composed of forest populations (F, 17/21 = 81%) whereas populationsthat jointhe dendrogramat higher Fst-values are mostly fromthe bocage (B, 14/20 = 70%). At Fst> 0.025 the contribution of the bocage populations is eightout of eight. Notethat populations thatjoin the dendrogram at the highest Fst-values are characterizedby mostly small effective population sizes (Ňe ≤ 10, indicated by small open dots). (B) Populations plotted along the first and second axis of a principal component analysis. The 23 forest populations are shown by small solid round symbols and the solid ellipse represents the mean ± standard deviation. Eighteenpopulations from the bocageare shown by large open round symbols, with the mean ± standard deviation shown bythe widerellipse with the interrupted line.

opencc-zeroJul 2021View details →

Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation

Microbial ecosystems harbor an astonishing diversity that can persist for long times. To understand how such diversity is structured and maintained, ecological and evolutionary processes need to be integrated at similar timescales. Here, we study a model of resource competition that allows for evolution via de novo mutation, and focus on rapidly adapting asexual populations with large mutational inputs, as typical of many bacteria species. We characterize the adaptation and diversification of an initially maladapted population and show how the eco-evolutionary dynamics are shaped by the interaction between simultaneously emerging lineages – clonal interference. We find that in large populations, more intense clonal interference can foster diversification under sympatry, increasing the probability that phenotypically and genetically distinct clusters coexist. In smaller populations, the accumulation of deleterious and compensatory mutations can push further the diversification process and kick-start speciation. Our findings have implications beyond microbial populations, providing novel insights about the interplay between ecology and evolution in clonal populations.

opencc-zeroApr 2023View details →

Data for: Simulated climate change causes asymmetric responses in insect life history timing potentially disrupting a classic ecological speciation system

Climate change may alter phenology within populations with cascading consequences for community interactions and ongoing evolutionary processes. Here, we measured the response to climate change in two sympatric, recently diverged (~170 years) populations of Rhagoletis pomonella flies specialized on different host fruits (hawthorn and apple) and their parasitoid wasp communities. We tested whether warmer temperatures affect dormancy regulation and its consequences for synchrony across trophic levels and temporal isolation between divergent populations. Under warmer temperatures, both fly populations developed earlier. However, warming significantly increased the proportion of maladaptive pre-winter development in apple, but not hawthorn, flies. Parasitoid phenology was less affected, potentially generating ecological asynchrony. Observed shifts in fly phenology under warming may decrease temporal isolation, potentially limiting ongoing divergence. Our findings of complex sensitivity of life-history timing to changing temperatures predict that coming decades may see multifaceted ecological and evolutionary changes in temporal specialist communities.