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35 results for “evolutionary distinctiveness”
Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks
<p>This Data set contain 29 table of weighted interaction network between plants (columns) and frugivore birds from the Brazilian Atlantic Forest used in the manuscript "Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks" published in Oikos Journal.</p>
Intracellular infection of ecologically important diatom species by an evolutionary distinct relative of the Fungi
<p>Data and R script from the publication "Intracellular infection of ecologically important diatom species by an evolutionary distinct relative of the Fungi":</p> <p>-plotting_and_testing_association.r: R script for the s.tatistical testing of NCLC1-diatom associations.</p> <p>-OSD_protist_ASV_table.csv: Amplicon Sequence Variant (ASV) table, comma separated. Lists the distribution of 7766 ASVs across 145 samples collected during the Ocean Sampling Day (OSD) 2014.</p> <p>-OSD_protist_ASV_sequences.fasta: fasta nucleotide file of the 7766 V4-18S ASVs sequenced as part of OSD and classified as unicellular eukaryotes ('protists'; re-processed in the present publication via DADA2).</p> <p>-sparCC_analysis.tar.gz: gzip'd archive with results from co-occurrence analyses ran on the protist OSD V4-18S dataset using sparCC (OSD_protist_ASV_sparCC_cor.csv: correlation output; OSD_protist_ASV_sparCC_100perm_pvals_twosided.csv: results of two-sided t-tests based on 100 sparCC permutations).</p> <p>-holomycota_alignment.fasta: multiple sequence alignment of reference holomycota 18S.</p> <p>-holomycota_MLtree_100nonparamboot.nwk: 18S maximum likelihood tree inferred using IQ-Tree; branch supports assessed with 100 non-parametric bootstrap replicates.</p> <p> </p>
Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums
<p>Interspecific hybridization can lead to adaptation and speciation, especially in the context of recent radiations. The emblematic <em>Crocodylus</em> (true crocodiles) is the most broadly distributed, ecologically diverse, and species-rich crocodylian genus. Nonetheless, their within-species evolutionary processes are poorly resolved mainly due to their potential for hybridization. Notably, the evolutionary outcomes when hybridization is ancient and involves long-lived species, like crocodiles, remain largely unexplored. Here, we evaluate the genomic admixture between the American (<em>Crocodylus</em> <em>acutus</em>) and the Morelet's (<em>Crocodylus</em> <em>moreletii</em>) species, and demonstrate that this hybridization system challenges the definition of species boundaries and poses a triple conservation conundrum: what has been recognized as <em>C. acutus</em> is actually two distinct species, therefore its taxonomic reassessment is needed; we identified two evolutionary distinct hybrids lineages, which are genetically discernible from the parental species; the remaining <em>C. moreletii </em>populations evidence its likely extinction as a species and/or evolution via hybridization. Hence, the crocodiles' distinct species and hybrids lineages warrant recognition and need urgent conservation efforts.</p>
Fig. 5 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 5. Representative ideogram of chromosomal pairs in Hypostomus cf. wuchereri showing the banding pattern after digestion using Alu I, Bam HI, Hae III, and Dde I. (a) population from Una River, (b) population from Mutum River.
Fig. 3 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 3. Chromosomal pairs of Hypostomus cf. wuchereri from Una River showing the C-bands and the digestion profiles using Alu I, Hae III, Dde I, and Bam HI.
Fig. 1 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 1. Karyotypes of Hypostomus cf. wuchereri. (a) population from Mutum River, (b) population from Una River. In detail, the NOR-bearing pair after silver nitrate (Ag-NOR) and C-banding (CB).
Fig. 2 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 2. Chromosomal pairs of Hypostomus cf. wuchereri from Mutum River showing the C-bands and the digestion profiles using Alu I, Hae III, Dde I, and Bam HI.
Fig. 4. DAPI and CMA 3 in Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence
Fig. 4. DAPI and CMA 3 stained chromosomal pairs from Mutum (a) and Una (b) Rivers, showing AT and GC-rich sites, respectively. The NOR-bearing pair is highlighted.
Data from: Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)
<p>The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well-understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines, and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.</p>
Data from: Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)
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Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums
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Data from: Unravelling the distinctive craniomandibular morphology of the Plio‐Pleistocene Eumysops in the evolutionary setting of South American octodontoid rodents (Hystricomorpha)
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Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus
Comparative models used to predict species threat status can help to identify diagnostic features of species at risk. Such models often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel Bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology, and spatial data, to calculate latent extinction risk (potential for non-threatened species to become threatened), estimate the most important drivers of risk for individual species, and map spatial patterns in the effects of different predictors on extinction risk. This could be of value for proactive conservation decision-making based on the early identification of species and regions of potential conservation concern.
Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
<p>Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (<em>Oncorhynchus mykiss</em>) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.</p>
Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks
<p>Seed dispersal by animals is one of the most important ecological processes in tropical forests, entailing millions of years of evolutionary adaptations of plants and frugivorous animals forming networks of interactions that, ultimately, contribute to the resilience of such forests. We analyze 29 seed dispersal networks in the threatened Atlantic Forest biodiversity hotspot, with data on the frequency of feeding visits by birds to fruiting plants to answer: (1) which are the effects of forest cover and landscape connectivity on the maintenance of phylogenetic diversity (PD) of interacting birds and plants and the evolutionary distinctiveness of the interactions (EDi) between them; and (2) how EDi and plant/bird PD affects the robustness of the interaction networks? We found that forest cover positively influences both plant and bird PD and EDi. Landscape connectivity is an important predictor of bird PD, but not plant PD, suggesting that the spatial arrangement of forest remnants is essential for guaranteeing bird movement among forest fragments. Furthermore, interaction networks of areas with higher PD and EDi had great robustness to the simulated extinction of species, which underscore the importance of larger forest blocks for conserving evolutionary information and, consequently, the health and natural resistance of seed dispersal networks against environmental change.</p>
Shared evolutionary origin and clade-specific signatures of symbiosis in lifestyle distinctive fungi
<p>Data repository established for the appendix dataset documented in Scarlet M. Au’s MPhil in Biological Science (Plant Sciences) thesis, submitted to the University of Cambridge, UK. </p> <p><strong>Appendix A.</strong> List of 182 species from the Mucoromycota subphylum</p> <p><strong>Appendix B.</strong> List of 535 BUSCO single copy genes identified for single copy phylogenies. </p> <p>1) Appendix B-1 contains BUSCO genes mostly annotated relative to the <em>Rhizophagus irregularis </em>DAOM_181602_v1.0. For genes that were missing, annotations were drawn from the Lyc-1 and the <em>Thamnidium elegans</em> genomes. </p> <p>2) Appendix B-2 contains BUSCO genes annotated relative to the <em>Rhizophagus irregularis </em>DAOM_181602_v1.0 genome. </p> <p>3) Appendix B-3 contains BUSCO genes annotated relative to the Lyc-1 genome.</p> <p>4) Appendix B-4 contains BUSCO genes annotated relative to the <em>Thamnidium elegans</em> genome. </p> <p><strong>Appendix C.</strong> Hierarchical clustering by orthogroup absence/presence and abundance. </p> <p>1) Full hierarchical clustering by row (species) and columns (orthogroups) for binary matrix. </p> <p>2) Full hierarchical clustering by row (species) and columns (orthogroups) for normalised matrix. </p> <p>3) Full hierarchical clustering by row (species) only for binary matrix. </p> <p>4) Full hierarchical clustering by row (species only) for normalised matrix.</p> <p><strong>Appendix D. </strong>36 out of 72 orthogroups shared between MFRE and AM fungal genomes contain known functional annotations. </p> <p> </p>
Similar Enzymatic Functions in Distinct Bioluminescence Systems: Evolutionary Recruitment of Sulfotransferases in Ostracod Light Organs
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Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus
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Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks
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Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
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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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