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Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasise how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.
Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
Data from: Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage
Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages.
Data from: Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot
The complex orogenic history and structure of Southern South America, coupled with Pleistocene glacial cycles, have generated paleoclimatic and environmental changes that influenced the spatial distribution and genetic composition of natural populations. Despite the increased number of phylogeographic studies in this region and given the frequent idiosyncratic phylogeographic patterns, there is still the need to focus research especially on species that are currently distributed within a wide range of bioclimatic regimes, and that historically have been subject to contrasting scenarios. Liolaemus tenuis is a widely distributed lizard species inhabiting latitudinally in almost 1,000 km through central and southern Chile. Here we describe the geographical patterns of genetic variation and lineage diversification within L. tenuis, and their association with geography and Pleistocene glaciations, using sequences from one mitochondrial and two nuclear genes, and five microsatellite loci, and covering most of the species distributional range. Our results revealed a high diversity both within and among populations, as well as two phylogeographic breaks, which are consistent with two of the larger rivers of central Chile, the Maipo and Biobío Rivers. Liolaemus tenuis is characterized by several allopatric lineages, especially in its north and central range, which suggest a history of multiple vicariance processes. Conversely, populations found in the southern range, south of the Biobío River, show signatures of recent decreases in effective population sizes, coupled with recent range expansions and secondary contact. Niche "envelope" data are consistent with patterns of genetic variation; both suggest a history of discontinuous areas of relatively stable populations throughout all of the distribution of L. tenuis. These data are also consistent with higher probabilities of habitat suitability north of the Maipo River (ca. 33°S), in both coastal areas and the "Intermediate Depression" between 34° - 37°S, as well as in the southern Coastal Cordillera between the Biobío and Araucanía regions. Interestingly, both molecular and niche envelope modelling data suggest that some populations may have persisted in fragmented refugia in Andean valleys, within the limits of the ice sheet. Finally, our results suggest that several populations of L. tenuis colonized glaciated regions from refugial areas in lowlands and coastal regions, and in the southern distribution, historic migration events would have occurred from refugial areas within the limits of the ice sheet.
Data from: Evidence of widespread topoclimatic limitation for lower treelines of the Intermountain West, U.S.A.
Many forests in dry mountain regions are characterized by a lower elevational treeline. Understanding the controls on the position of lower treeline is important for predicting future forest distributional shifts in response to global environmental change. Lower treelines currently at their climate limit are expected to be more sensitive to changing climate, whereas lower treelines constrained by non-climatic factors are less likely to respond directly to climate change but may be sensitive to other global change agents. In this study, we used existing vegetation classifications to map lower treelines for our 1.7 million km2 study region in the Intermountain West, USA. We modeled topoclimatic drivers of lower treeline position for each of three dominant forest types to identify topoclimatically-limited treelines. We then used spatial data of edaphic properties, recent fire, and land use to identify lower treelines potentially constrained above their ecophysiological limits by non-climatic processes. We found that the lower treeline ecotone of pinyon-juniper woodlands is largely limited by topoclimate and is likely to be sensitive to increasing temperatures and associated droughts, though these effects may be heterogeneously distributed across the landscape. In contrast, dry mixed conifer lower treelines in the northern portion of the study area rarely reached their modeled topoclimatic limit, suggesting that non-climatic processes, including fire and land use, constrain lower treeline above its ecophysiological limits in this forest type. Our results suggest that much of the lower treeline in the Intermountain West is currently climate-limited and will thus be sensitive to ongoing climate changes. Lower treelines in other arid or semi-arid mountainous regions around the globe may also be strongly sensitive to climate, though treeline response to climate change will be mediated at the local scale by soil properties, biotic interactions, and natural or anthropogenic disturbances. Our regional study of lower treeline provides a framework for identifying the drivers of lower treeline formation and allows for more robust projections of future treeline dynamics, which are needed to anticipate shifting global distributions of the forest biome.
Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
Data from: Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation
A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history, and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions, and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction-site associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.
Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
FIGURE 20–29 in A new widespread European bee species of the genus Dasypoda Latreille (Hymenoptera, Apoidea)
FIGURE 20–29. Structure of the galea (lateral view): 20–21. Dasypoda morawitzi sp. nov.; 22–23. D. hirtipes; 24–25. D. sinuata; 26–27. D. oraniensis; 28. D. albipila; 29. D. tubera; (20, 22, 24, 26—females; scale = 0.2 mm; 21, 23, 25, 27–29— males; scale = 0.5 mm).
FIGURE 9–19 in A new widespread European bee species of the genus Dasypoda Latreille (Hymenoptera, Apoidea)
FIGURE 9–19. Males of Dasypoda morawitzi sp. nov. Different forms of color pubescence (left [9–12] and right [13–16] specimens were caught simultaneously at the same place of Tsyurupinsk district of Kherson region, Ukraine; 17–19— holotype): 9, 13. Male in dorsal view (scale = 5 mm); 10, 14, 17. Male in lateral view (scale = 5 mm); 11, 15. Metasoma in ventral view (scale = 2 mm); 12, 16, 18. Head in frontal view (scale = 1 mm); 19. Vertex of head (scale = 0.5 mm).
FIGURES 5A–5B. Cochylis notulana Zeller, 1847 lectotype male genitalia. Fig. 5A in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 5A–5B. Cochylis notulana Zeller, 1847 lectotype male genitalia. Fig. 5A: male genitalia (phallus removed). Fig. 5B: Phallus.
FIGURE 9 in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURE 9. Neighbor-Joining tree (Kimura 2 Parameter model) of Phalonidia and Gynnidomorpha COI (DNA barcode) sequences. The scale bar indicates 1% sequence difference.
FIGURES 6A–6B in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 6A–6B. Cochylis udana Guenée, 1845 lectotype male genitalia. Fig. 6A: male genitalia (phallus removed). Fig. 6B: Phallus.
FIGURES 1A–1F. Adult specimens. Fig. 1A in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 1A–1F. Adult specimens. Fig. 1A: Phalonidia udana male (Finland). Fig. 1B: Phalonidia udana male (Finland), Fig. 1C: P. m a n n i a n a male (Finland), Fig. 1D: P. m a n n i a n a male (Austria), Fig. 1E: P. m a n n i a n a male (Germany), Fig. 1F: P. manniana male (Germany).
FIGURES 8A–8C in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 8A–8C. Holotype of Phalonidia tolli Razowski, 1960. Fig. 8A: adult male. Fig. 8B: male genitalia (phallus removed). Fig. 8C: Phallus.
FIGURES 3A-3C. Female genitalia. Fig. 3A, 3B in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 3A-3C. Female genitalia. Fig. 3A, 3B: Phalonidia udana. Fig. 3C: P. manniana. 3A, genitalia slide NHMO 2065; 3B, genitalia slide NHMO 2066; 3C, genitalia slide LAA 2011.015.
FIGURE 10 in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURE 10. Maximum Likelihood phylogenetic tree of Cochylini, based on COI sequences. The tree is rooted to Tortrix viridana (Tortricidae, Tortricini). Node bootstrap support values are indicated by the nodes.
FIGURE 7 in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURE 7. Comparison of valvae of Phalonidia manniana and P. udana with C. notulana lectotype, C. udana lectotype and P. tolli holotype included.
FIGURES 2A-2G. Male genitalia. Fig. 2A–2D in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species
FIGURES 2A-2G. Male genitalia. Fig. 2A–2D: Phalonidia udana. Fig. 2E–2H: P. m a n n i a n a. 2A–2B, genitalia slide NHMO 2063; 2C–2D, genitalia slide NHMO 2068; 2E–2F, genitalia slide NISK 20003; 2G–2H, genitalia slide NHMO 2064. 2B, 2D, 2F, 2H show the phallus of the preparations.
FIGURE 2 in Redescription of Astyanax guianensis Eigenmann 1909 (Characiformes: Characidae), a poorly known and widespread fish from the Amazon, Orinoco and Guiana Shield drainages
FIGURE 2. Upper and lower jaws of Astyanax guianensis (medial view, right side), MZUSP 109674, 46.7 mm SL. Coronomeckelian bone is missing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.