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74 results for “evolutionary processes”
Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species
<p>Background and Aims Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localised species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40 km 2 area of Sydney, Australia and is threatened by increased urbanisation. Eucalyptus sp. Cattai is yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted. Methods We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status. Key Results All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridisation was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids. Conclusions Multiple evolutionary processes (e.g., hybridisation and clonality) can operate within the one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.</p>
Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics
<p class="western">Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (<i>Abies</i>, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of <i>π</i><sub>a</sub>/<i>π</i><sub>s</sub> and <i>K</i><sub>a</sub>/<i>K</i><sub>s</sub> with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.</p>
Data from: Evolutionary process of extremely twisted heteromorph ammonites from the Upper Cretaceous in Japan
<p><span>The heteromorph ammonite </span><em><span>Pravitoceras sigmoidale</span></em><span> with extremely twisted retroversal hook and its probable ancestors, </span><em><span>Didymoceras awajiense</span></em><span> and </span><em><span>D</span><span>. </span><span>morozumii</span></em><span>, occur mainly in the Upper Cretaceous Izumi and Sotoizumi groups in southwest Japan. Their morphological characteristics were investigated in this study. Morphotypes I–II were recognized in </span><em><span>D. morozumii</span></em><span>. Morphotypes III–V were recognized in </span><em><span>D. awajiense</span></em><span>. Morphotypes VI–VIII were recognized in </span><em><span>P. sigmoidale</span></em><span>. Moreover, all morphotypes were recognized in both the dextral and sinistral forms of these three species. Based on the morphological and stratigraphic relationships, it is considered that the evolutionary process of these species is divided into three steps: (1) shift from morphotypes I–II to III; (2) increase in variation from morphotypes III to III–V; and (3) shift from morphotypes III–V to VI–VIII. By comparing these morphotypes based on the 'growing tube model' belonging to the moving frame analysis, it is seen that there are no significant gaps of coiling patterns in the evolutionary processes of this lineage. Meanwhile, morphotypes III–V of </span><em><span>D. awajiense</span></em><span> have a larger morphological variation than morphotypes I–II of </span><em><span>D</span><span>. </span><span>morozumii</span></em><span><em> </em>and morphotypes VI–VIII of </span><em><span>P. sigmoidale</span></em><span>. These results, and the radiometric ages from previous studies, suggest that </span><em><span>D. awajiense</span></em><span>, with considerable variation between ancestor and descendant species, existed in a short interval. It seems that </span><em><span>P. sigmoidale</span></em><span> occurred after the continuous but rapid and drastic morphological evolution from </span><em><span>D. morozumii</span></em><span><em> </em>via<em> </em></span><em><span>D. awajiense</span></em><span>.</span></p>
Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)
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Data from: The roles of ecological and evolutionary processes in plant community assembly: the environment, hybridization and introgression influence co-occurrence of Eucalyptus
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Data from: Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)
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Data from: Evolutionary processes, dispersal limitation and climatic history shape current diversity patterns of European dragonflies
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Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics
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Data from: Proteomic evidence of a paedomorphic evolutionary process within a marine snail species: a strategy for adapting to extreme ecological conditions?
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Data from: Evolutionary process of extremely twisted heteromorph ammonites from the Upper Cretaceous in Japan
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Evolutionary and ecological processes influence a plant-bumble bee network
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Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species
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What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?
<p>Major Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey in a stickleback metapopulation to test predictions derived from each of these hypotheses. We identify over a thousand MHCIIβ variants (alleles spanning paralogous genes) and find that many of them covary positively or negatively with parasite load, suggesting that these genes contribute to resistance or susceptibility. However, despite our large sample-size, we find no evidence for the widely-cited stabilizing selection on MHC heterozygosity, in which individuals with an intermediate number of MHC variants have the lowest parasite burden. Nor do we observe a rare-variant advantage, or widespread fluctuating selection across populations. In contrast, we find that MHC diversity is best predicted by neutral genome-wide heterozygosity and between-population genomic divergence, suggesting neutral processes are important in shaping the pattern of metapopulation MHC diversity. Thus, although MHCIIβ is highly diverse and relevant to the type and intensity of macroparasite infection in these populations of stickleback, the main models of MHC evolution still provide little explanatory power in this system.</p>
Data from: Evolutionary patterns and processes: lessons from ancient DNA
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
Data from: Inference of evolutionary jumps in large phylogenies using Lévy processes
While it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis.
Data from: A common-garden experiment to quantify evolutionary processes in copepods: the case of emamectin benzoate resistance in the parasitic sea louse Lepeophtheirus salmonis
Background:The development of pesticide resistance represents a global challenge to food production. Specifically for the Atlantic salmon aquaculture industry, parasitic sea lice and their developing resistance to delousing chemicals is challenging production. In this study, seventeen full sibling families, established from three strains of Lepeophtheirus salmonis displaying differing backgrounds in emamectin benzoate (EB) tolerance were produced and quantitatively compared under a common-garden experimental design. Lice surviving to the preadult stage were then exposed to EB and finally identified through the application of DNA parentage testing. Results: With the exception of two families (19 and 29%), survival from the infectious copepod to preadult stage was very similar among families (40-50%). In contrast, very large differences in survival following EB exposure were observed among the families (7.9-74%). Family survival post EB exposure was consistent with the EB tolerance characteristics of the strains from which they were established and no negative effect on infection success were detected in association with increased EB tolerance. Two of the lice families that displayed reduced sensitivity to EB were established from a commercial farm that had previously used this chemical. This demonstrates that resistant alleles were present on this farm even though the farm had not reported treatment failure. Conclusions: To our knowledge, this represents the first study where families of any multi-cellular parasite have been established and compared in performance under communal rearing conditions in a common-garden experiment. The system performed in a predictable manner and permitted, for the first time, elucidation of quantitative traits among sea lice families. While this experiment concentrated on, and provided a unique insight into EB sensitivity among lice families, the experimental design represents a novel methodology to experimentally address both resistance development and other evolutionary questions in parasitic copepods.
Data from: Investigating the timing of origin and evolutionary processes shaping regional species diversity: insights from simulated data and Neotropical butterfly diversification rates
Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ("how" and "why" of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.
Data from: Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild
The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life histories components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies.
Data from: Inference of evolutionary jumps in large phylogenies using Lévy processes
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What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?
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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.