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382 results for “Adaptive radiation”
Adaptive radiation of pelagiarian fishes at the K/Pg boundary led to rapid diversification of mandible morphology
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Ecological opportunity spurred adaptive radiation of Central Mexican Silversides: Evidence from functional and morphometric traits
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Data from: Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards
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Data from: Different traits dominate evolution at early and late stages of adaptive radiation
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Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats
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Data from: Evolution across the adaptive landscape in a hyperdiverse beetle radiation
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Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock
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Online appendix for: Hybridization and transgressive evolution as drivers of adaptive radiations: Reticulate evolution generates diversity in the Puerto Rican Anolis lizards
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Data from: We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation
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Data for: Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation
<p>Data for:</p> <p>Houde P, Braun EL, Zhou L. 2020. Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation. Diversity, in review</p> <p>**************************************************<br> The .tar.gz file will expand to yield a directory named "Houde_Braun_Zhou_data_files". That directory has three subdirectories:</p> <p>1. alignments<br> 2. indel_matrices<br> 3. trees</p> <p>The Houde_Braun_Zhou_data_files directory also includes a README.txt file with complete details regarding the contents of each subdirectory.</p>
Data from: Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
<p><b>Background:</b> Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts' biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of extremely young adaptive radiations of Nicaraguan Midas cichlid fish (<i>Amphilophus</i> cf. <i>citrinellus</i>) from two crater lakes to test the hypothesis that parallel divergence in trophic ecology is associated with parallel changes of the gut microbiota.</p> <p><b>Results:</b> Bacterial communities of the water and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology.</p> <p><b>Conclusions:</b> Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.</p>
Data from: The propagation of admixture-derived adaptive radiation potential
<p>Adaptive radiations frequently show remarkable repeatability where single lineages undergo multiple independent episodes of adaptive radiation in distant places and long separate timepoints. Increasing evidence suggests that genetic variation generated through hybridization between distantly related lineages can promote adaptive radiation. This mechanism, however, requires rare coincidence in space and time between the hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only in the site where it occurred and the elevated genetic variation will persist only for a short period. Hence, hybridization seems unlikely to explain recurrent adaptive radiation in the same lineage. Contrary to these expectations, our evolutionary computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if certain conditions are present such that ecological and/or geographic mechanisms split the hybrid population into isolated sub-lineages. Subsequent secondary hybridization of some of these can reestablish genetic polymorphisms from the ancestral hybridization in places far from the birthplace of the hybrid-clade and long after the ancestral hybridization event. Consequently, simulations revealed conditions where exceptional genetic variation, once generated through a rare and unlikely hybridization event, can facilitate multiple adaptive radiations exploiting ecological opportunities available at distant points in time and space.</p>
Data from: The ecological and genomic basis of explosive adaptive radiation
<p>Rates of speciation vary tremendously among evolutionary lineages, with our understanding of what fuels the rapid succession of speciation events within young adaptive radiations remaining particularly incomplete. The cichlid fish family provides the most notable example of such variation among extant metazoans. It includes many slowly speciating lineages as well as the several exceptionally large and rapid adaptive radiations. By reconstructing a large phylogeny of all described cichlid species, we show that explosive speciation is solely concentrated in several large yet young lake species flocks. Across the family, speciation rate increases are associated with absence of top predators, and speciation rate decreases are associated with arid climate, but these factors are not nearly sufficient to explain explosive speciation in lake radiations, in particular the Lake Victoria adaptive radiation. Across lake radiations we observe a positive relationship between speciation rate and enrichment with large indel polymorphisms. Assembly of one hundred Victorian cichlid genomes comprising all extant ecological guilds and taxonomic genera reveals this radiation contains exceptional 'genomic potential' - hundreds of ancient haplotypes bearing indel polymorphisms, many of which are strongly associated with specific ecologies and are shared with ecologically similar species from other older lake radiations elsewhere in Africa. Network analysis reveals fundamentally non-treelike evolution through recombining old haplotypes, with origins of ecological guilds concentrated early in the Victoria radiation. Our results suggest that the combination of ecological opportunity, sexual selection and exceptional genomic potential is the key to understanding explosive adaptive radiation.</p>
Data from: Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defences and modifying host tissues to favour brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype–environment association analysis and phenotypic characterization of growth rate under different temperatures. We found that genetic variation and population structure within each species is best explained by distinct spatial and environmental variables. We observed both common (temperature seasonality and the host species) and distinct (drought, cold stress, precipitation) environmental and spatial factors that shaped the genomes of these fungi resulting in contrasting outcomes. Phenotypic intraspecific variations in Grosmannia clavigera and Leptographium longiclavatum, together with high heritability, suggest potential for adaptive selection in these species. By contrast, Ophiostoma montium displayed narrower intraspecific variation but greater tolerance to extreme high temperatures. Our study highlights unique phenotypic and genotypic characteristics in these symbionts that are consistent with our hypothesis. By maintaining this multipartite relationship, the bark beetles have a greater likelihood of obtaining the benefits afforded by the fungi and reduce the risk of being left aposymbiotic. Complementarity among species could facilitate colonization of new habitats and survival under adverse conditions.
Data from: Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids
Background: Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a broad adaptive landscape. However only a handful of studies have actually investigated the adaptive landscape and its implication for our interpretation of the underlying mechanisms of phenotypic evolution. In fishes the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification during an adaptive radiation given its implications for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. Results: We use multivariate ordination models of phenotypic evolution and posterior predictive approaches to investigate the adaptive landscape and test for evidence of early diversification of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by divergent selection towards two distinct adaptive peaks and the early divergence of modern morphological disparity. Evolutionary models and posterior predictive approaches favoured constant-rate divergent selection over decreasing rates of phenotypic evolution as the underlying process driving the early divergence of locomotor phenotypes. Conclusions: The influence of multiple adaptive peaks on the divergence of locomotor attributes in Geophagini is compatible with the expectations of an ecologically-driven adaptive radiation. This study confirms that the diversification of locomotor morphology represents an important dimension of phenotypic evolution in the geophagine adaptive radiation. It also suggests that the commonly observed early burst of phenotypic evolution during adaptive radiations is best explained by a model that incorporates divergent selection deep in the phylogeny.
Data from: Testing for ancient adaptive radiations in Neotropical cichlid fishes
Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether patterns of lineage and morphological diversification are congruent with hypothesized adaptive radiations in South and Central America. We found that diversification in the Neotropical cichlid clade and the highly diverse tribe Geophagini was consistent with diversity-dependent, early bursts of divergence followed by decreased rates of lineage accumulation. South American Geophagini underwent early rapid differentiation in body shape, expanding into novel morphological space characterized by elongate-bodied predators. Divergence in head-shape attributes associated with trophic specialization evolved under strong adaptive constraints in all Neotropical cichlid clades. The South American Cichlasomatini followed patterns consistent with constant rates of morphological divergence. Although morphological diversification in South American Heroini was limited, Eocene invasion of Central American habitats was followed by convergent diversification mirroring variation observed in Geophagini. Diversification in Neotropical cichlids was influenced by the early adaptive radiation of Geophagini, which potentially limited differentiation in other cichlid clades.
Data from: Origins of female genital diversity: predation risk and lock-and-key explain rapid divergence during an adaptive radiation
The study of male genital diversity has long overshadowed evolutionary inquiry of female genitalia, despite its non-trivial diversity. Here we identify four non-mutually exclusive mechanisms that could lead to genital divergence in females, and potentially generate patterns of correlated male-female genital evolution: (1) ecological variation alters the context of sexual selection ("ecology hypothesis"), (2) sexually antagonistic selection ("sexual-conflict hypothesis"), (3) female preferences for male genitalia mediated by female genital traits ("female-choice hypothesis"), and (4) selection against inter-population mating ("lock-and-key hypothesis"). We performed an empirical investigation of all four hypotheses using the model system of Bahamas mosquitofish inhabiting blue holes that vary in predation risk. We found unequivocal support for the ecology hypothesis, with females exhibiting a smaller genital opening in blue holes containing piscivorous fish. This is consistent with stronger postmating female choice/choice when predators are present, but greater premating female choice in their absence. Our results additionally supported the lock-and-key hypothesis, uncovering a pattern of reproductive character displacement for genital shape. We found no support for the sexual conflict or female choice hypotheses. Our results demonstrate a strong role for ecology in generating female genital diversity, and suggest that lock-and-key may provide a viable cause of female genital diversification.
Data from: Ecological opportunity and diversification in a continental radiation of birds: climbing adaptations and cladogenesis in the Furnariidae
Ecological theories of adaptive radiation predict that ecological opportunity stimulates cladogenesis through its effects on competitive release and niche expansion. Given that key innovations may confer ecological opportunity, we investigate the effect of the acquisition of climbing adaptations on rates of cladogenesis in a major avian radiation, the Neotropical bird family Furnariidae, using a species-level phylogeny. Morphological specializations for vertical climbing originated in the woodcreepers ca. 23 Mya, well before that adaptation occurred in woodpeckers (Picidae) or in other potential competitors in South America. This suggests that the acquisition of climbing adaptations conferred ample ecological opportunity to early woodcreepers. Nonetheless, we found that increases in speciation rates in Furnariidae did not coincide with the acquisition of climbing adaptations, and that the relationship between the accumulation of climbing adaptations and rates of speciation was negative. In addition, we did not detect a diversity-dependent decline in woodcreeper diversification rates consistent with saturation of the trunk-climbing niche. These findings do not support the hypothesis that ecological opportunity related to trunk-foraging stimulated cladogenesis in this radiation. The negative effect of climbing on diversification may be mediated by an indirect positive effect of climbing on dispersal ability, which may reduce speciation rates over evolutionary time scales.
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: Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities.
Because island communities are derived from the mainland, they are often less diverse by comparison. However, reduced complexity of island communities can also present ecological opportunities. For example, amphibian diversity on the Indonesian island of Sulawesi is generally lower than in the Philippines, but this island supports a surprisingly diverse endemic assemblage of Sulawesi fanged frogs (genus Limnonectes). To explore evolutionary dynamics of this system, we examined molecular, morphological, and geographical variation of fanged frogs from these two regions. Using genealogical concordance – a conservative standard – we identified 12 species on Sulawesi, only four of which are described. One more species can be distinguished with morphology, and a Bayesian approach to species delimitation suggests our total species estimate on Sulawesi (n = 13) is still an underestimate. After accounting for evolutionary history, a model with multiple body size optima in sympatric Limnonectes species is significantly preferred over a "random walk" model where body size evolves by Brownian motion. Additionally, morphological variation is higher among sympatric than non-sympatric species on Sulawesi, but not in the Philippines. Taken together, these findings suggest that adaptive radiation of fanged frogs on Sulawesi was driven by natural selection to infiltrate ecological niches occupied by other lineages in the Philippines. Our study supports the concept of ecological opportunity in community assembly: diversification in mature communities, such as the Philippines, is limited by a dearth of unoccupied ecological niches. On Sulawesi however, evolutionary novelties originated in a predictable and replicated fashion in response to opportunities presented by a depauperate ancestral community.
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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)
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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.