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66 results for “parallel divergence”
Data from: Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska
Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbor similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.
Data from: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations
Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages. We find a strong signature of increasing genomic divergence with time in both the mitochondrial genome and the nuclear genome. In contrast to many other systems, we find that in these cichlids regions of elevated relative differentiation also exhibit increased absolute differentiation. We detect a signature of convergent evolution in a comparison of outlier regions across all three species pair comparisons but the extent of it is modest, and regions that are strongly divergent in any one pair tend to be only slightly elevated in the other pairs, consistent with a repeatable but polygenic basis of traits that characterize the ecomorphs. Our results suggest that strong functional phenotypic differentiation, as seen in all three species pairs, is generally associated with a clear signature of genomic divergence, even in the youngest species pair.
Data from: Parallel allochronic divergence in a winter moth due to disruption of reproductive period by winter harshness
The disruption of reproductive timing by climatic harshness may result in the temporal isolation of conspecific populations and, ultimately, in speciation. However, whether temporal isolation alone can act as the force initiating speciation and how often the same type of climatic disruption results in the divergence of allochronic populations in a lineage is largely unknown. The reproductive period of the winter geometrid moth Inurois punctigera is separated into early and late winter in habitats with severe winters, but not in habitats with mild winters, suggesting that the reproductive season is disrupted by the harshness of the mid-winter period. Here, we show that sympatric pairs of early- and late-winter populations that differ in origin exist in different regions, suggesting a parallel divergence of reproductive timing. In each region, significant genetic differentiation exists between these early- and late-winter populations, suggesting that the temporal reproductive isolation has persisted. Moreover, we demonstrate that the temporal isolation, in comparison with geographic isolation, contributes greatly to the genetic differentiation among geographic and temporal populations by an analysis of molecular variances and a comparison of genetic differentiations (Fst) between geographic populations with and without difference in reproductive season. Thus, adaptive divergence of allochronically reproducing populations occurred independently in different regions, implying the generality of speciation by temporal isolation in a winter moth lineage.
Data from: Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets
When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket <i>Laupala</i>. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and the likelihood that sharing QTL is related to phenotypic effect sizes. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.
Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities among ecotype-pairs on three close islands (< 10 km distance) connected by weak gene flow (Nm~0.03) and with recent common ancestry (< 10,000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared among all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
Data from: Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved "dwarf" and "normal" sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with all five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation, and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further examination of the links between this critical physiological pathway and ecological and genetic variation will provide insight into the fine-scale evolutionary dynamics at work in nature.
Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40. in Viverridae
Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40.
Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on FST values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows
Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 6. The maximum-likelihood phylogram for cytochrome oxidase subunit I (COI) haplotypes. Bootstrap support and Bayesian posterior probabilities are shown. Normal font indicates reference haplotypes, bold font indicates haplotypes obtained in present study.
Figure 3 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 3. Shells of Belgrandiella: (a–f) molecular clade A: (a–d) Belgrandiella cf. robusta, spring of river LipsenjŠČica, Cerknica; (e, f) Belgrandiella cf. robusta, Dvorce, Čatež ob Savi; (g) Boleana umbilicata, topotype, spring MoČilnik; (h, i) molecular clade B: Belgrandiella cf. kuesteri, PotoČe; (j–r) molecular clade C: (j) Belgrandiella cf. fontinalis, PotoČe; (k–r) Belgrandiella cf. fontinalis, Babja luknja; (s, t) molecular clade D: Belgrandiella cf. koprivnensis, Izvor Plive 1A, DraganiĆ. Scale bar represents 1 mm.
Figure 2 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 2. Shells of Belgrandiella (molecular clade A): (a–c) Belgrandiella kusceri, topotype, Rakek; (d, e) Belgrandiella zermanica, topotype, Zrmanja River; (f, g) Belgrandiella krupensis, topotype, Krupa River; (h–j) Belgrandiella cf. fontinalis, Krk Island; (k, l) Belgrandiella robusta, topotype, Veliki Obrh; (m, n) Belgrandiella cf. pageti, KrŠka jama, source of Krka River; (o) Belgrandiella cf. robusta, ŽerovniŠČica; (p–s) Belgrandiella cf. croatica, Rupa na Brodu. Scale bar represents 1 mm.
Figure 1 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 1. Localities of the studied Belgrandiella and geographic distribution of clades (see Figures 6 and 7).
Figure 5 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 5. Penes of Belgrandiella: (a) Belgrandiella cf. fontinalis, Babja luknja (molecular clade C); (b–d) Belgrandiella robusta, Obrh, type locality (molecular clade A). Scale bar represents 0.5 mm.
Figure 7. The maximum-likelihood phylogram for H3 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 7. The maximum-likelihood phylogram for H3 haplotypes. Bootstrap support and Bayesian posterior probabilities are shown.
Figure 4 in A case of biodiversity overestimation in the Balkan Belgrandiella A. J. Wagner, 1927 (Caenogastropoda: Hydrobiidae): molecular divergence not paralleled by high morphological variation
Figure 4. Renal and pallial section of female reproductive organs of Belgrandiella: (a) Belgrandiella fontinalis, Babja luknja (molecular clade C); (b) Belgrandiella robusta, Obrh, type locality (molecular clade A) (bc, bursa copulatrix; cbc, duct of bursa copulatrix; ga, albuminoid gland; gn, nidamental gland; gp, gonoporus; ov, oviduct; ovl, loop of oviduct; rec, rectum; rs, receptaculum seminis). Scale bar represents 1 mm.
Data from: Molecular phenotyping of maternally mediated parallel adaptive divergence within Rana arvalis and Rana temporaria
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Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
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