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35 results for “historical effects”
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
<p>Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation likely accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.</p>
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
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Replication package for: The real effects of monetary expansions: evidence from a large-scale historical experiment
<p>The replication materials contain a README file, STATA datasets and do-files. This replication package for Palma (2021) constructs the entire analysis from the data sources described in the published paper, using STATA. The replicator should expect the code to run for less than 10 minutes.</p> <p>Palma, N. (2021). The real effects of monetary expansions: evidence from a large-scale historical experiment. Review of Economic Studies, forthcoming</p> <p> </p>
Data from: Historical fire regimes and contemporary fire effects within sagebrush habitats of Gunnison Sage-grouse
<p>The historical role of fire in sagebrush (<em>Artemisia</em> <em>tridentata</em>) landscapes remains poorly understood yet is important to inform management and conservation of obligate species such as the threatened Gunnison Sage-grouse (GUSG; <em>Centrocercus</em> <em>minimus</em>). We reconstructed fire histories from tree-ring fire-scars at sagebrush-forest ecotones (10 sites, 111 trees) to better understand the role of fire in sagebrush landscapes of the Upper Gunnison Basin (UGB), Colorado, and how fire may have changed following European-American settlement. We assessed likely influences of historical fire by surveying plant composition and structure at 100 sagebrush sites with and without recent (2001–2020) fire. </p> <p>Tree-ring fire-scars revealed a history of repeated low-severity fire at sagebrush-forest ecotones until 1892, followed by over a century without fire. Between 1684 and 1892, the mean fire interval (MFI) among sites averaged 41.3 years (ranging from 18.2 to 79.7 years). Fire over this period occurred synchronously at two or more sites on average every 23.6 years, consistent with spread between sites. Most (70%) of the historical fires burned in the early growing season when strong winds can spread fire through sagebrush. Recent burns, relative to unburned sites exhibited greater reductions in sagebrush (<em>Artemisia</em> <em>tridentata</em>; 27% vs. 6%) and concomitant increases in herbaceous (40% vs. 55%) cover. These differences declined with time since fire but persisted for at least two decades. Burns were dominated by a suite of native perennial grasses, forbs, and a re-sprouting shrub species. Historically, such openings may have served as seasonal GUSG habitat. Burns exhibited slightly increased cover (4% vs. 1%) of a widely-planted non-native perennial grass, crested wheatgrass (<em>Agropyron</em> <em>cristatum</em>). </p> <p>Our results suggest that parts of the UGB sagebrush landscapes were characterized historically by frequent fire and dynamic vegetation mosaics that included open, grassy patches. These findings are consistent with the use of prescribed fire to restore and maintain this ecological process and vegetation heterogeneity. However, the contemporary context for fire has changed, and now includes substantially reduced (Endangered Species Act) ESA-listed GUSG populations, increased risk of non-native plant invasion, and climate warming. These circumstances highlight new risks, information needs, and opportunities for key knowledge co-production via management-research partnerships. </p>
Historical effects during experimental evolution of multicellularity in <em>Saccharomyces cerevisiae</em>
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A dataset of hydrological effects induced by historical and modern earthquakes in the Southern Apennines of Italy
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Data from: Historical fire regimes and contemporary fire effects within sagebrush habitats of Gunnison Sage-grouse
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Data from: Human−geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan
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Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections
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Current climate overrides historical effects on species richness and range size of freshwater plants in Europe and North America
<p>1. The latitudinal diversity gradient (LDG) hypothesis suggests that species richness should be highest at low latitudes, whereas Rapoport's rule states that largest ranges ought to be found for species at high latitudes. However, there is no consensus over these patterns and their underlying drivers in the freshwater realm.</p> <p>2. We investigated species richness and mean range size of freshwater plants in 50 km × 50 km grid cells across Europe (40°N to 71°N) and North America (25°N to 78°N), supplemented with data based on 1° latitudinal bands for mean range size. We were especially interested to find out whether there are similarities and differences in these ecogeographical patterns and their underlying drivers between the continents due to their contrasting historical characteristics, spatial extent and topography. </p> <p>3. First, we used partial regression to reveal whether species richness and mean range size of freshwater plants have a linear or quadratic relationship with latitude. Second, we employed variation partitioning based on partial regression to model relationships between plant species richness and mean range size and four explanatory variable groups (i.e., environmental features, current climate, historical climate and geographical location). Third, we utilized boosted regression tree analysis to further investigate species richness and mean range size of freshwater plants in relation to a set of explanatory variables. </p> <p>4. Our results revealed that species richness showed relatively similar patterns in relation to latitude between the continents. Similarly, mean range size trends were alike in North America whether we used 50 km x 50 km grid cell data or 1° latitudinal bands. Instead, different patterns in mean range size emerged between the used data sets in Europe. For both of species richness and mean range size, current climate (with different individual predictor variables) was the main driver in both the continents, but historical effects had a small influence on the response variables.</p> <p>5. <i>Synthesis</i>. Our findings indicated that major ecogeographical rules can strongly vary for the same taxonomic group across broad scales between continents. It is also premature to rely solely on well-known terrestrial taxonomic groups when drawing generalizations about ecogeographical rules.</p>
Data from: The effect of historical legacy on adaptation: do closely related species respond to the environment in the same way?
The many documented examples of parallel and convergent evolution in similar environments are strong evidence for the role of natural selection in the evolution of trait variation. However, species may respond to selection in different ways; idiosyncrasies of their evolutionary history may affect how different species respond to the same selective pressure. To determine whether evolutionary history affects trait-environment associations in a recently diverged lineage, we investigated within-species trait-environment associations in the white proteas, a closely related monophyletic group. We first used MANOVAs to determine the relative importance of shared response to selection, evolutionary history, and unique responses to selection on trait variation. We found that on average, similar associations to the environment across species explained trait variation, but that the species had different mean trait values. We also detected species-specific associations of traits to the environmental gradients. To identify the traits associated uniquely to the environment we used a structural equation model. Our analysis showed that the species differed in how their traits were associated with each of the environmental variables. Further, in the cases of two root traits (root mass and root length:mass ratio), two species differed in the direction of their associations (e.g. populations in one species had heavier roots in warmer areas, and populations in the other species had lighter roots in warmer areas). Our study shows that even in a closely related group of species, evolutionary history may have an effect on both the size and direction of adaptations to the environment.
Data from: Unravelling the effects of contemporary and historical range expansion on the distribution of genetic diversity in the damselfly Coenagrion scitulum
Although genetic diversity provides the basic substrate for evolution, there are a limited number of studies that assess the impact of recent climate change on intraspecific genetic variation. This study aims to unravel the degree to which historical and contemporary factors shape genetic diversity and structure across a large part of the range of the range-expanding damselfly Coenagrion scitulum (Rambur, 1842). A total of 525 individuals from 31 populations were genotyped at nine microsatellites, and a subset was sequenced at two mitochondrial genes. We inferred the importance of geography, environmental factors, and recent range expansion on genetic diversity and structure. Genetic diversity decreased going westwards, suggesting a signature of historical post-glacial expansion from east to west and the presence of eastern refugia. Although genetic differentiation decreased going northwards, it increased in the northern edge populations, suggesting a role of contemporary range expansion on the genetic make-up of populations. The phylogeographical context was proven to be essential in understanding and identifying the genetic signatures of local contemporary processes. Within this framework, our results highlight that recent range expansion of a good disperser can decrease genetic diversity and increase genetic differentiation which should be considered when devising suitable conservation strategies.
Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. Results: We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Conclusions: Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.
Disentangling the contemporary and historical effects of landscape on population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil
<p class="MsoNormal"><span>Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (<em>Conopophaga cearae</em> and <em>Sclerurus cearensis</em>) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.</span></p>
Inverse priority effects: A role for historical contingency during species losses
<p>Communities worldwide are losing multiple species at an unprecedented rate, but how communities reassemble after these losses is often an open question. It is well established that the order and timing of species arrival during community assembly shapes forthcoming community composition and function. Yet, whether the order and timing of species losses can lead to divergent community trajectories remains largely unexplored. Here, we propose a novel framework that sets testable hypotheses on the effects of the order of species losses inverse priority effects and suggests its integration into the study of community assembly. We propose that the order of species losses within a community can generate alternative reassembly trajectories, and suggest mechanisms that may underlie these inverse priority effects. To formalize these concepts quantitatively, we used a three-species Lotka-Volterra competition model, enabling to investigate conditions in which the order of species losses can lead to divergent reassembly trajectories. The inverse priority effects framework proposed here promotes the systematic study of the dynamics of species losses from ecological communities, ultimately aimed to better understand community reassembly and guide management decisions in light of rapid global change.</p>
Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
Data from: Comparison of historical bottleneck effects and genetic consequences of reintroduction in a critically-endangered island passerine
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Data from: The effect of historical legacy on adaptation: do closely related species respond to the environment in the same way?
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Disentangling the contemporary and historical effects of landscape on population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil
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Inverse priority effects: A role for historical contingency during species losses
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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.