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79 results for “historical and contemporary”
Historical racial redlining and contemporary patterns of income inequality negatively affect birds, their habitat, and people in Los Angeles, California
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A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group
<p>Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer sequencing of air-dried cheilostomes, utilizing a recent library preparation method for low DNA input. We evaluate a <i>de novo</i> mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and or congenerics have been sequenced verify the appropriateness of our workflow and give confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.</p>
Data from: Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star Linckia laevigata
Marine animals inhabiting the Indian and Pacific oceans have some of the most extensive species ranges in the world, sometimes spanning over half the globe. These Indo-Pacific species present a challenge for study with both geographic scope and sampling density as limiting factors. Here, we augment and aggregate phylogeographic sampling of the iconic blue sea star, Linckia laevigata Linnaeus, 1758, and present one of the most geographically comprehensive genetic studies of any Indo-Pacific species to date, sequencing 392 base pairs of mitochondrial COI from 791 individuals from 38 locations spanning over 14,000 km. We first use a permutation based multiple-regression approach to simultaneously evaluate the relative influence of historical and contemporary gene flow together with putative barriers to dispersal. We then use a discrete diffusion model of phylogeography to infer the historical migration and colonization routes most likely used by L. laevigata across the Indo-Pacific. We show that estimates of genetic structure have a stronger correlation to geographic distances than to "oceanographic" distances from a biophysical model of larval dispersal, reminding us that population genetic estimates of gene flow and genetic structure are often shaped by historical processes. While the diffusion model was equivocal about the location of the mitochondrial most recent common ancestor (MRCA), we show that gene flow has generally proceeded in a step-wise manner across the Indian and Pacific oceans. We do not find support for previously described barriers at the Sunda Shelf and within Cenderwasih Bay. Rather, the strongest genetic disjunction is found to the east of Cenderwasih Bay along northern New Guinea. These results underscore the importance of comprehensive range-wide sampling in marine phylogeography.
Data from: Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm
Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.
Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia
We used a comparative approach to assess congruence of phylogeographic and genetic structure and diversity, demographic signals, and ratios of pollen to seed dispersal, in the context of species-specific life-history traits, for two widespread sympatric perennial plant species. We sampled Grevillea paradoxa and Melaleuca nematophylla across the species' ranges throughout the Transitional Rainfall Zone and extending slightly into the Arid Zone of south-west Western Australia. Both species exhibited range-wide phylogeographic and contemporary genetic structure. Moderate haplotype diversity centred in populations on Banded Ironstone Formation (BIF) outcrops and within the Murchison River gorge supports a hypothesis of historical persistence and evolution in these mesic refugia. These features are likely to play important roles in evolutionary persistence with ongoing climate change. There was little evidence of particularly complex demographic histories for the region. More limited haplotype diversity, as well as more limited nuclear genetic diversity and connectivity, in G. paradoxa was consistent with predictions from life-history traits of shorter lifespan, lower fecundity, more limited seed dispersal, and shorter plants, but inconsistent with a prediction of greater pollen dispersal by bird pollinators. Low pollen to seed dispersal ratios suggest seed dispersal plays a greater than expected role in maintaining connectivity in this semi-arid landscape. The study highlights a need for research that integrates aspects of seed ecology and seed and pollen dispersal as well as phylogeographic and genetic patterns in Gondwanan shrublands and other semi-arid landscapes globally.
Data from: Inferring contemporary and historical genetic connectivity from juveniles
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeting sampling in nurseries and juveniles aggregation should be included in the genomic toolbox of threatened species management.
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: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment
Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale-dependence of the determinants of diversity is broadly acknowledged, we here argue that limitation to a single analysis scale and data pseudoreplication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates an explicit accounting of past environmental variation and provides an appropriate measurement of richness. Due to environmental niche conservatism organisms generally reside in climatically defined bioregions, or "evolutionary arenas", characterized by in situ speciation and extinction. These bioregions differ in age and their total productivity and have varied over time in area and energy available for diversification. We show that, consistently across the four major terrestrial vertebrate groups, current-day species richness of the world's main 32 bioregions is best explained by a model that integrates area and productivity over geological time together with temperature. Adding finer-scale variation in energy availability as an ecological predictor of within-bioregional patterns of richness explains much of the remaining global variation in richness at the 110km grain. These results highlight the separate evolutionary and ecological effects of energy availability and provide a first conceptual and empirical integration of the key drivers of broad-scale richness gradients. Avoiding the pseudo-replication that impedes the evolutionary interpretation of non-hierarchical macroecological analyses, our findings integrate evolutionary and ecological mechanisms at their most relevant scales and offer a new synthesis regarding global diversity gradients.
Data from: The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)
Narrow endemics are at risk from climate change due to their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (ave Fst =0.14), and a north -south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest populations in the center of the range represent the point of entry to the Lake Michigan and a refugia of diversity for this species. A strong association between genetic distances and lake level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explain local patterns or movement.
Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification rates of the two moth assemblages. Finally, we explored the effects of contemporary ecological factors on diversity patterns.<b> </b>From 7788 specimens we identified to 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Overall, moths in YS mountains showed higher species diversity and phylogenetic diversity than in TH mountains. Ancestral range analysis indicated YS as the origin. Significant historical dispersals from YS to TH mountains were detected. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow, were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we showed that a combined analysis of diversity patterns at multiples scales, including community, population and species levels, incorporating both historical and contemporary factors, are very informative for understanding factors of shaping diversity patterns.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits
In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here.
Fig. 8 in Historical and Contemporary Occurrence ofCylindera(s. str.)celeripes(LeConte) (Coleoptera: Carabidae: Cicindelinae) and Implications for Its Conservation
Fig. 8. Historical and currently known geographical occurrence of Cylindera celeripes by county. Red = last record prior to 1920; orange = last record 1941–1960 ("?" = questionable record); green = last record 1991–1996; blue = last record 2005–2011.
Figs. 2–7 in Historical and Contemporary Occurrence ofCylindera(s. str.)celeripes(LeConte) (Coleoptera: Carabidae: Cicindelinae) and Implications for Its Conservation
Figs. 2–7. Habitats of Cylindera celeripes. 2) Western Iowa (Pottawattamie Co., Hitchcock Nature Center, Badger Trail); adults were active in moderately vegetated 2-track below road cut; 3) Northwestern Oklahoma (Woodward Co., Alabaster Caverns State Park, upper Nature Trail); adults were active amongst sparse vegetation in lichen-encrusted clay/gypsum exposures; 4) Northwestern Oklahoma (Major Co., Glass Mountains State Park); adults were active amongst sparse vegetation in lichen-encrusted clay/gypsum exposures on top of butte; 5) Northwestern Oklahoma (Major Co., Glass Mountains, vic. Scenic Overlook); adults were active in sparsely vegetated clay exposures in undisturbed areas of lower talus slopes and on top of neighboring butte; 6) Northwestern Missouri (Atchison Co., Star School Hill Prairie Natural Area, south tract); adults were seen amongst rather dense vegetated on upper slopes along the center foreground path; 7) Northwestern Missouri (Atchison Co., Brickyard Hill Conservation Area, High Creek Prairie); adults were active in sparsely vegetated clay exposures on and below lower slopes.
Fig. 1 in Historical and Contemporary Occurrence ofCylindera(s. str.)celeripes(LeConte) (Coleoptera: Carabidae: Cicindelinae) and Implications for Its Conservation
Fig. 1. Cylindera celeripes adults at: a) Hitchcock Nature Center, Pottawattamie Co., IA (13 July 2008); b) Alabaster Caverns State Park, Woodward Co., OK (10 June 2009); c) Same locality as "b", note parasite (possibly Hymenoptera: Dryinidae) protruding from abdomen and ant head attached to right antenna; d) Brickyard Hill Natural Area, Atchison Co., MO (27 June 2009).
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>
Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
<p><span>Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.</span></p>
FIG. 5 in Contemporary and Historical Species Relationships Reveal Assembly Mechanism Intricacies among Co-occurring Darters (Percidae: Etheostomatinae)
FIG. 5. Body shape relationships among darter species (PC1 vs. PC2) based on 12 homologous landmarks used in geometric morphometric analyses. The molecular phylogeny is overlaid to illustrate phylogenetic–morphological relationships among species. Gray wireframe warped grids show body shape extremes along PC1 (48.25% of variation) and PC2 (18.85% of variation). All warped grids are magnified 2.5 times in order to better illustrate changes in variation across each axis. Darter line drawings depict E. blennioides (lower left in morphospace) and N. rufilineatus (upper right in morphospace), and each shows the locations of the 12 homologous landmarks included. Phylogenetic niche conservatism of PC1 (determined by Blomberg's K value) can be visualized in the figure.
FIG. 2 in Contemporary and Historical Species Relationships Reveal Assembly Mechanism Intricacies among Co-occurring Darters (Percidae: Etheostomatinae)
FIG. 2. Map of Duck River drainage showing the 15 study sites. Inserted panel depicts an overview of the location of the Duck River drainage in Tennessee, USA.
FIG. 4 in Contemporary and Historical Species Relationships Reveal Assembly Mechanism Intricacies among Co-occurring Darters (Percidae: Etheostomatinae)
FIG. 4. Ultrametric tree including all darter species known to occur in the Duck River drainage (regional species pool). Species present at each site are illustrated as circles, and abundances are represented by size of circles (i.e., circle sizes are sqrt transformed abundances). For reference, the greatest abundance of a species collected from a single site during the study was E. zonale (site nine; n ¼ 43). Different circle shades represent the different species. Sites one through 15 are depicted from upstream to downstream (left to right). Encircled nodes indicate the two main clades in which species were phylogenetically clustered. See Data Accessibility for tree file.
FIG. 3 in Contemporary and Historical Species Relationships Reveal Assembly Mechanism Intricacies among Co-occurring Darters (Percidae: Etheostomatinae)
FIG. 3. Scatterplots depicting relationships between assemblages and degree of clustering or evenness based on the Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) standard effect size metrics (SESmetrics). Positive values indicate phylogenetic clustering and negative values indicate phylogenetic evenness. NRI values are black circles and NTI values are open triangles (*indicate significant phylogenetic structure in assemblages [P 0.05]). (A) Depicts analyses based on species presence/absence within each assemblage, and (B) depicts analyses including weighted abundances, and therefore indicates relationships among individuals within assemblages.
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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.