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98 results for “habitat adaptation”
Data from: Juvenile divergence in adaptive traits among seven sympatric fish eco-morphs arises before moving to different lacustrine habitats
Identifying the mechanisms initiating sympatric diversification in vertebrates has remained a conceptual challenge. Here we analyze an assemblage of sympatric charr (Salvelinus malma) morphs from landlocked Lake Kronotskoe basin as a model to uncover the divergence pathways in freshwater fishes during the early life history stages. All morphs have distinct developmental biology, but a similar developmental rate retardation compared to the ancestor. Our study reveals that adult morphological differences, which acquire functionality at maturation, originate in the early juvenile stages due to heterochrony in skeletogenesis and allometric changes triggered by variation in metabolic activity. The craniofacial differences among the morphs result from asynchronous development of several skeletal modules. The accelerated ossification of teeth-armed bones occurs in predatory feeding morphs, while cranial cover ossification is promoted in benthivorous morphs. These contrasting growth patterns have led to seven phenotypes that span a range far beyond the ancestral variability. The most distinct morphs are a riverine-spawning, epilimnetic predator and a lacustrine-spawning, profundal benthic feeder. Taken together, we argue that the adaptive morphological differentiation in these sympatric freshwater fishes is driven by diverging patterns in ossification rate and metabolic activity against a background of uneven somatic growth. This divergence is primarily associated with basic environmental differences on the nursery grounds that might be unrelated to resource use. This non-heritable phenotype divergence is then exposed to natural selection that could result in further adaptive genetic changes.
Data from: Adaptive morphological shifts to novel habitats in marine sculpin fishes
Sculpin fishes of the North American Pacific Coast provide an ideal opportunity to examine whether adaptive morphological character shifts have facilitated occupation of novel habitat types because of their well-described phylogeny and ecology. In this group, the basal-rooted species primarily occupy the subtidal habitat, whereas the species in the most distal clades are found in the intertidal. We tested multiple evolutionary models to determine whether changes in body size and changes in number of scales are adaptive for habitat use in sculpins. Based on a statistically robust, highly resolved molecular phylogeny of 26 species of sculpins, in combination with morphometric and habitat affinity data, our analyses show that an adaptive model based on habitat use best explains changes in body size and number of scales. The habitat model was statistically supported over models of neutral evolution, stabilizing selection across all habitats, and three clade-based models. We suggest that loss of scales and reduction of body size in the intertidal may facilitate cutaneous breathing in air when tidepools become hypoxic during low tides. This study demonstrates how the combined use of phylogenetic, ecological and statistical approaches helps to identify traits that are likely adaptive to novel habitats.
Data from: Gene regulatory divergence between locally adapted ecotypes in their native habitats
Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally-adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally-adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (GxE interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.
Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation
Among the World's most challenging environments for plant life is the Atacama Desert, an arid zone extending over 1300 km and from sea level to 2000/3000 m along the southwestern Andean foothills. Plants there and in the adjacent Mediterranean zone exhibit striking adaptations, and we here use a species-rich such group to address the question whether adaptations arose in parallel, at different times, or simultaneously. Answering this type of question has been a major concern of evolutionary biology over the past few years, with a growing consensus that lineages tend to be conservative in their vegetative traits and niche requirements. Combined nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900 aligned nucleotides) yielded a fossil-calibrated phylogeny that includes 43 of the 54 species of Oxalis occurring in Chile. Distribution models (SDMs) for these species that included precipitation, temperature, fog and/or vegetation types and the phylogeny were used to reconstruct ancestral habitat preferences, relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we used a background sample from 1224 Chilean Oxalis collections to correct models for collecting effort. Models with just 10 of 19 bioclim parameters did as well as more parameter-rich models. Results reveal that the Oxalis flora of Chile consists of seven distant lineages that originated at different times prior to the last Andean uplift pulse and some of which had features pre-adapting them to seasonally arid or xeric conditions. The Mediterranean core zone, south of the Atacama, offered an ecological refuge for insufficiently arid-adapted species and harbors a mix of ancient and young groups. There is no evidence of rapid adaptive radiation.
Data from: Interspecific variation in the structural properties of flight feathers in birds indicates adaptation to flight requirements and habitat
1. The functional significance of intra- and interspecific structural variations in the flight feathers of birds is poorly understood. Here, a phylogenetic comparative analysis of four structural features (rachis width, barb and barbule density and porosity) of proximal and distal primary feathers of 137 European bird species was conducted. 2. Flight type (flapping and soaring, flapping and gliding, continuous flapping or passerine type), habitat (terrestrial, riparian or aquatic), wing characteristics (wing area, S and aspect ratio, AR) and moult strategy were all found to affect feather structure to some extent. Species characterized by low wing-beat frequency flight (soaring and gliding) have broader feather rachises (shafts) and feather vanes with lower barb density than birds associated with more active flapping modes of flight. However, the effect of flying mode on rachis width disappeared after controlling for S and AR, suggesting that rachis width is primarily determined by wing morphology. 3. Rachis width and feather vane density are likely related to differences in force distribution across the wingspan during different flight modes. An increase in shaft diameter, barb density and porosity from the proximal to distal wing feathers was found and was highest in species with flapping flight indicating that aerodynamic forces are more biased towards the distal feathers in flapping flyers than in soarers and gliders. 4. Habitat affected barb and barbule density, which was greatest in aquatic species, and within this group, barb density was greater in divers than non-divers, suggesting that the need for water repellency and resistance to water penetration may influence feather structure. However, we found little support for the importance of porosity in water repellency and water penetration, because porosity was similar in aquatic, riparian and terrestrial species and among the aquatic birds (divers and non-divers). We also found that barb density was affected by moult pattern. 5. Our results have broad implications for the understanding of the selection pressures driving flight feather functional morphology. Specifically, the large sample size relative to any previous studies has emphasized that the morphology of flight feathers is the result of a suite of selection pressures. As well as routine flight needs, constraints during moulting, habitat (particularly aquatic) and migratory requirements also affect flight feather morphology. Identifying the exact nature of these trade-offs will perhaps inform the reconstruction of the flying modes of extinct birds.
Data from: Gut microflora may facilitate adaptation to anthropic habitat: a comparative study in Rattus
Anthropophilic species ('commensal' species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their non-commensal counterparts. Using a next-generation-sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 non-commensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the non-commensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.
Data from: Wolves adapt territory size, not pack size to local habitat quality
1. Although local variation in territorial predator density is often correlated with habitat quality, the causal mechanism underlying this frequently observed association is poorly understood and could stem from facultative adjustment in either group size or territory size. 2. To test between these alternative hypotheses, we used a novel statistical framework to construct a winter population-level utilization distribution for wolves (Canis lupus) in northern Ontario, which we then linked to a suite of environmental variables to determine factors influencing wolf space use. Next, we compared habitat quality metrics emerging from this analysis as well as an independent measure of prey abundance, with pack size and territory size to investigate which hypothesis was most supported by the data. 3. We show that wolf space use patterns were concentrated near deciduous, mixed deciduous/coniferous and disturbed forest stands favoured by moose (Alces alces), the predominant prey species in the diet of wolves in northern Ontario, and in proximity to linear corridors, including shorelines and road networks remaining from commercial forestry activities. 4. We then demonstrate that landscape metrics of wolf habitat quality – projected wolf use, probability of moose occupancy and proportion of preferred land cover classes – were inversely related to territory size but unrelated to pack size. 5. These results suggest that wolves in boreal ecosystems alter territory size, but not pack size, in response to local variation in habitat quality. This could be an adaptive strategy to balance trade-offs between territorial defence costs and energetic gains due to resource acquisition. That pack size was not responsive to habitat quality suggests that variation in group size is influenced by other factors such as intraspecific competition between wolf packs.
Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite
Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host–pathogen interactions. Yet, we lack empirical data to translate the theory to natural host–parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0–40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host–parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health.
Data from: Rapid adaptive phenotypic change following colonization of a newly restored habitat
Real-time observation of adaptive evolution in the wild is rare and limited to cases of marked, often anthropogenic, environmental change. Here we present the case of a small population of reed warblers (Acrocephalus scirpaceus) over a period of 19 years (1996–2014) after colonizing a restored wetland habitat in Malta. Our data show a population decrease in body mass, following a trajectory consistent with a population ascending an adaptive peak, a so-called Ornstein–Uhlenbeck process. We corroborate these findings with genetic and ecological data, revealing that individual survival is correlated with body mass, and more than half of the variation in mean population fitness is explained by variation in body mass. Despite a small effective population size, an adaptive response has taken place within a decade. A founder event from a large, genetically variable source population to the southern range margin of the reed warbler distribution likely facilitated this process.
Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)
Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fish by sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of Jcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genes therein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.
Data from: Adaptive trait divergence of annual plants in response to urban habitat diversity in a megacity
<p>Data from the common garden experiment, field environmental factors, and data for Qst-Fst comparisons.</p>
Dataset from: Parapatric and sympatric adaptation of Setaria viridis populations in Japan to heterogeneous coastal habitats via trait divergence of plant form, salt spray tolerance and flowering time
<p>This study aimed to determine how coastal variants of<em> </em>plants arise from local populations under natural selection by studying variations in phenotypic variations and survival of <em>Setaria viridis</em> populations inhabiting mosaic environments of two seashores in Japan. <em>S.viridis</em> populations comprised five coastal variants showing significantly higher salt spray tolerance than the inland variant: ST, short and tolerant (common variant); TM, tall and mid-tolerant (Inland Sea); TT, tall and tolerant; PT, prostrate and tolerant; L, extremely late flowering; I, inland and susceptible variants. These variations imply that maritime plants first acquired salt spray tolerance for survival, after which compact plants evolved in habitats where strong winds caused damage from salt spray. Results indicate that diverse intensities of salt spray and winds as well as summer drought generated various coastal variations in parapatry and sympatry.</p>
Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925). in Muridae
Distribution. Now restricted to the Channel Country of SW Queensland and the Lake Eyre Basin in NE South Australia. Descriptive notes. Head-body 95-120 mm, tail 105-160 mm, ear 23-29 mm, hindfoot 32-37 mm; weight 30-50 g. The Fawn Hopping Mouse has body form typical of hopping mice, with very long hindfeet, long tail with distal brush of longer hairs, very long ears, and large protruberant eyes. Dorsal fur is of variable color, from pale pinkish fawn to gray; ventral fur white. Unlike most other hopping mice, it has no throat pouch, but males have a glandular area of naked skin on the chest. Habitat. Occurs in low shrublands and tussock grasslands on stony ("gibber") plains and claypans. Shows marked habitat segregation from the Dusky Hopping Mouse (N. fuscus), which is closely associated with sandy substrates. Food and Feeding. The Fawn Hopping Mouse is mostly granivorous, but also eats other plant material (stems, leaves) and occasionally invertebrates. It uses succulent, salt-adapted plants around edges of claypans as a source of water. Breeding. Reproduction is probably largely opportunistic and aseasonal, with high reproductive output from near-continuous breeding after periods of high rainfall; reported littersize is 1-5, most commonly three; gestation period 38-43 days for nonlactating females. Females may mature later than other hopping mice, with reproductive maturity reached at about six months. Activity patterns. Terrestrial and nocturnal. Fawn Hopping Mice shelter during day in burrow systems that are typically simpler and shallower than those of other hopping mice. Movements, Home range and Social organization. Fawn Hopping Mice generally live singly or in small groups; typically uncommon within range, but population density may increase by an order of magnitude following periods of high rainfall. Status and Conservation. Classified as Near Threatened on The IUCN Red List. The Fawn Hopping Mouse has shown marked decline in range (estimated at greater than 50%), and presumably population size, since European settlement of Australia. This is mostlikely due to predation by the introduced house cat and Red Fox (Vulpes vulpes), and to habitat degradation associated with pastoralism. Bibliography. Brazenor (1934), Burbidge et al. (2008), Finlayson (1939), Gould (1853), Jackson & Groves (2015), Murray et al. (1999), Ogilby (1892), Thomas (1921h), Van Dyck & Strahan (2008), Waite (1898), Watts & Aslin (1981), Woinarski et al. (2014), Wood Jones (1925).
Performance-based habitat choice can drive rapid adaptive divergence and reproductive isolation - Data
<p>Data for Performance-based habitat choice can drive rapid adaptive divergence and reproductive isolation</p>
Habitat Escalated Adaptive Therapy (HEAT), With Neoadjuvant Radiation for Soft Tissue Sarcoma
ClinicalTrials.gov study NCT05301283. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Interspecific variation in the structural properties of flight feathers in birds indicates adaptation to flight requirements and habitat
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Data from: Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub
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Data from: Adaptive morphological shifts to novel habitats in marine sculpin fishes
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Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite
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Data from: Gut microflora may facilitate adaptation to anthropic habitat: a comparative study in Rattus
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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.