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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 1. Shells.A–J in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 1. Shells.A–J, Pupilla alpicola (A–E, lowland populations"P.pratensis"; F–J, typical mountain populations).K–P, P.loessica. Q–T, P. muscorum. A, M_6001_3_1, Lake Galenbeck (Mecklenburg-Western Pomerania, Germany). B, SMNS-ZI0138340, type locality Dinkelscherben near Augsburg (Bavaria, Germany). C, M_846_1_2, Burgtonna (Thuringia, Germany), fossil from Early
Figure 6 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 6. Thin-plate splines illustrating (theoretical) transitions in shape, side view, exaggeration 5 times. A, fossil P. loessica → extant P. loessica. B, fossil P. pratensis (including P. m. densegyrata) → extant P. pratensis. C, fossil P. pratensis (including P. m. densegyrata) → extant P. alpicola. D, extant P. pratensis → P. alpicola. E, extant P. loessica→ P. alpicola. F, fossil P. muscorum → extant P. muscorum.
Figure 8 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 8. Phylogenetic tree based on COI. 50% majority rule consensus tree from Bayesian analysis with posterior probabilities/bootstrap support values (from maximum likelihood analysis). Sample abbreviations and groups of samples are given in Tables 1 and 3.
Figure 11 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 11. Pupa muscorum var. pratensis. Series of four shells from type locality Dinkelscherben near Augsburg (Germany) in frontal and lateral view. A, neotype SMNS-ZI0138339. B–D, SMNS-ZI0138341.
Figure 10 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 10. Pupilla loessica. Series of four shells from type locality Předmostí at Přerov (Czech Republic, fossil from Saalian loess) in frontal and lateral view. A is the designated neotype. All deposited at the National Museum of Prague.
Figure 7 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 7. Shell microsculpture (SEM micrographs). A–T, P. loessica. U–Z, P. alpicola. a–d, P. alpicola (morphogroup P. m. densegyrata). e–h, P. alpicola (lowland populations "P. pratensis"). i–j, P. muscorum. A–B, M_4559, Altai, Saylyugem (Russia). C–D, M_4575, Altai, Saylyugem (Russia). E–F, H_MC409, Altai, Dzhazator (Russia). G–H, M_3970, Khatgal, shore of Lake Khövsgöl Nuur (northern Mongolia). I–J, M_2523_2, Yelantsy near Lake Baikal (Russia). K–L, M_2523_1, Yelantsy near Lake Baikal (Russia). M–N, M_994, Karsdorf (Saxony Anhalt, Germany), fossil from Early Saalian. O–P, M_459, Zeuchfeld (Saxony
Figure 9 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)
Figure 9. Phylogenetic tree based on ITS2. 50% majority rule consensus tree from Bayesian analysis with posterior probabilities/bootstrap support values (from maximum likelihood analysis). Sample abbreviations and groups of samples are given in Tables 1 and 3.
Figure 4 in Mosaic patterns of homoplasy accompany the parallel evolution of suspensory adaptations in the forelimb of tree sloths (Folivora: Xenarthra)
Figure 4. Geometric morphometric principal components analysis of the ulna, humerus and scapula of xenarthrans. A, the first two axes of the ulna GM analysis. No other principal components (PC) axis accounts for more than 5% of variation. B, the first two axes of the humerus GM analysis. The small amount of variation accounted for by PC2 is likely due to the small sample sizes for the taxa it differentiates, specifically armadillos, the two giant ground sloths, and to a lesser extent Hapalops. PC3 accounts for 5.6% of variation and differentiates Cyclopes from Paramylodon and Glossotherium. No other axes account for more than 5% of variation. C, the first two PCs of the scapula GM analysis. PCs 3 and 4 account for 8.6% and 6.3% of variation, respectively. PC 3 separates Cyclopes from other taxa, and PC 4 separates Cyclopes and Dasypus from Choloepus. No other PC accounts for more than 5% of variation. Sloth scapula specimens identified with a thick rimmed circle and black dot indicate the specimens shown in 4D. D, Choloepus (centre) has a relatively conserved gross scapular morphology (compare with Paramylodon on right), especially when compared with Bradypus (left), but it has mapped functional traits such as an angled scapular spine onto that conserved bauplan. Squares indicate armadillos, rounded squares indicate anteaters, and circles indicate sloths.
Figure 5 in Mosaic patterns of homoplasy accompany the parallel evolution of suspensory adaptations in the forelimb of tree sloths (Folivora: Xenarthra)
Figure 5. Geometric morphometric phylomorphospace of the ulna, humerus and scapula. A, phylomorphospace of the ulna shows that tree sloths inhabit the same region of morphospace, suggesting extensive parallel evolution relative to their last common ancestor, while giant ground sloths and armadillos diverged in the opposite direction and anteaters appear to have diverged little from the last
Figure 1 in Mosaic patterns of homoplasy accompany the parallel evolution of suspensory adaptations in the forelimb of tree sloths (Folivora: Xenarthra)
Figure 1. Phylogeny used in this study showing the relationships among living xenarthrans and extinct sloths based on recent molecular studies (see methods for details on how the tree was constructed). Extant tree sloths are labelled in purple. Hapalops and Acratocnus have been argued to show adaptations for arboreality, although these adaptations might also reflect digging habits. Other sloths are almost certainly terrestrial based on size. None of these forms show adaptation to suspensory behaviours and thus it is likely that this morphobehavioural suite evolved independently in living sloths. A cross symbol (†) indicates an extinct taxon.
Data from: Molecular phenotyping of maternally mediated parallel adaptive divergence within Rana arvalis and Rana temporaria
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Data from: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations
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Parallel molecular mechanisms for enzyme temperature adaptation
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Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
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Data from: Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish
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Data from: Adaptive plasticity and genetic divergence in feeding efficiency during parallel adaptive radiation of whitefish (Coregonus spp.)
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Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower
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Data from: Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
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Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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