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121 results for “darter”
Data from: Do river drainage boundaries coincide with phylogeographic breaks in the redband darter?
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Data from: The role of ecology in allopatric speciation of darters in the Central Highlands, USA
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A new species of bridled darter endemic to the Etowah River system in Georgia (Percidae: Etheostomatinae: Percina)
<p>"alignments" folder contains concatenated ddRAD phylip alignments produced by iPyrad. `mXXp` naming scheme consistent with iPyrad parameter files.</p> <p>"bridledCOB.nex" contains the DNA sequence alignment for the mtDNA gene cytochrome b used in the Bayesian phylogenetic analysis. </p> <p>"bridledCOB.nex.con.tre" summarized posterior tree from Bayesian analysis of the mtDNA cytochrome b data.</p> <p>"bridledNUC.nex" contains the DNA sequence alignment for the 11 nuclear genes used in the Bayesian phylogenetic analysis.</p> <p>"bridledNUC.nex.con.tre" summarized posterior tree from Bayesian analysis of the 11 nuclear genes.</p> <p>"fastqs" folder contains demultiplexed fastq files containing ddRAD reads for each individual.</p> <p>"iPyrad_paramFiles" folder contains assembly parameters for iPyrad. `mXXp` indicates the minimum proportion of samples per locus (`min_samples_locus` iPyrad parameter). For example, `m70p` indicates that each locus is represented by at least 70% of the samples. </p> <p>"P_freemanorum_meristic_data.csv" the merstic data of Percina freemanorum.</p> <p>"P_freemanorum_meristic_specimen_info.csv" information associated with specimens of Percina freemanorum.</p> <p>"P_kusha_meristic_data.csv" the merstic data of Percina kusha.</p> <p>"P_kusha_meristic_specimen_info.csv" information associated with specimens of Percina kusha.</p> <p>"IQTree" folder contains bash script to run IQTree analyses and resulting treefiles. `mXXp` naming scheme consistent with iPyrad parameter files.</p> <p>"VCFs" folder contains bash script to run VCFTools filtering, outgroup file listing outgroup taxa to prune, input VCF file from iPyrad, and filtered VCF files. `Unlinked` indicates that SNPs have been pruned to include only one SNP per ddRAD locus. `mXXp` naming scheme consistent with iPyrad parameter files.<br> </p>
A new species of bridled darter endemic to the Etowah River system in Georgia (Percidae: Etheostomatinae: Percina)
<p><i>Percina freemanorum</i>, the Etowah Bridled Darter, is described as a new species endemic to the Etowah River system in Georgia, specifically in Long Swamp Creek, Amicalola Creek, and the upper portion of the Etowah River. The earliest collection records for <i>Percina freemanorum</i> date to 1948 and in 2007 the species was delimited as populations of <i>Percina kusha</i>. Our investigation into the systematics of <i>Percina kusha</i> is motivated by the uncertain status of populations in the Coosawattee River system and observed morphological disparity in several meristic traits between populations in the Conasauga and Etowah River systems. Our analyses of morphological divergence, nuclear genotypes, and mtDNA haplotype networks confirm the distinctiveness of <i>Percina freemanorum</i>. Morphologically, <i>Percina freemanorum</i> is distinguished from <i>Percina kusha</i> through lower average numbers of lateral line scales (65.4 vs. 72.3); rows of transverse scales (18.0 vs. 21.4); scales around the caudal peduncle (22.1 vs. 24.9); and modally more pectoral fin rays (14 vs. 13). The two species are not reciprocally monophyletic in phylogenetic analysis of mtDNA sequences, but the two species do not share mtDNA haplotypes. Analysis of up to 158,000 RADseq loci resolve each of the two species as reciprocally monophyletic and genomic clustering analysis of single nucleotide polymorphisms identifies two genetic clusters that correspond to the morphologically delimited <i>Percina freemanorum</i> and <i>Percina kusha</i>.</p>
Data from: The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae)
Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life-history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life-history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna.
FIGURE 2. Crystallaria cincotta, 75 in Crystallaria cincotta, a new species of darter (Teleostei: Percidae) from the Elk River of the Ohio River drainage, West Virginia
FIGURE 2. Crystallaria cincotta, 75 mm SL male, Elk River, West Virginia.
FIGURE 1 in Crystallaria cincotta, a new species of darter (Teleostei: Percidae) from the Elk River of the Ohio River drainage, West Virginia
FIGURE 1. Box truss network of 23 distances used in morphometric analysis of Crystallaria.
Data from: Epigenetic divergence as a potential first step in darter speciation
Recent studies show that epigenetic variation in the form of DNA methylation may serve as a substrate for selection. Theory suggests that heritable epigenetic marks that increase fitness should increase in frequency in a population, and these changes may result in novel morphology, behaviour, or physiology, and ultimately reproductive isolation. Therefore, epigenetic variation might provide the first substrate for selection during the course of evolutionary divergence. This hypothesis predicts that populations in the earliest stages of divergence will differentiate in their methylome prior to any genetic differentiation. While several studies have investigated natural epigenetic variation, empirical studies that test predictions about its role in speciation are surprisingly scarce. Here, we investigate DNA methylation variation using an isoschizomeric digest method, Methyl-Sensitive Amplified Polymorphism, across multiple stages of evolutionary divergence in natural populations of North American stream fishes. We show that epigenetic differentiation between methylomes is greater than genetic divergence among closely related populations across two river drainages. Additionally, we demonstrate that epigenetic divergence is a stronger predictor of the strength of behavioural reproductive isolation and suggest that changes in the methylome could influence the evolution of reproductive isolation between species. Our findings suggest a role for epigenetics not only in the initiation of divergence, but also in the maintenance of species boundaries over greater evolutionary timescales.
Fig. 6 in Life-history of the South American darter, Characidium pterostictum (Crenuchidae): evidence for small scale spatial variation in a piedmont stream
Fig. 6. Seasonal variation of mean condition factor (K) of Characidium pterostictum in the Lajeado river (southern Brazil). PA, upstream site; PB, downstream site. * In PA no specimen was captured in Summer.
Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments
<p>Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.</p>
FIG. 6 in Redescription of the Guiana Shield Darter Species Characidium crandellii and C. declivirostre (Crenuchidae) with Descriptions of Two New Species
FIG. 6. Distribution of Characidium crandellii, type locality indicated with T.
Data from: The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae)
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Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments
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Data from: Epigenetic divergence as a potential first step in darter speciation
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A new species of bridled darter endemic to the Etowah River system in Georgia (Percidae: Etheostomatinae: Percina)
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Spatail gradient approach application in assessing changes in the rainbow darter (Etheostome caeruleum) liver transcriptome in the Grand River, Ontario
GEO Series GSE95082. Etheostoma caeruleum. 63 samples. Type: Expression profiling by array.
Temporal changes in the rainbow darter (Etheostome caeruleum) liver transcriptome associated with sewage treatment plant upgrades in the Grand River, Ontario
GEO Series GSE95083. Etheostoma caeruleum. 79 samples. Type: Expression profiling by array.
FIGURE 5 in Three new darter species of the Etheostoma percnurum species complex (Percidae, subgenus Catonotus) from the Tennessee and Cumberland river drainages
FIGURE 5. Photographs of a live (A) male and (B) female E. lemniscatum, Big South Fork Cumberland River, showing typical color and pigmentation of females and non-nuptial males. Photographs by M. R. Thomas, 2008.
FIG. 10 in Redescription of the Guiana Shield Darter Species Characidium crandellii and C. declivirostre (Crenuchidae) with Descriptions of Two New Species
FIG. 10. Lateral view (top) of Characidium duplicatum, new species, in life and dorsal, lateral, and ventral views after preservation, CSBD F-3614, holotype, 39.4 mm SL. Photos by J. W. Armbruster.
Getting inside of the molecular pathways associated with intersex in the rainbow darter (Etheostoma caeruleum)
GEO Series GSE57394. Etheostoma caeruleum. 28 samples. Type: Expression profiling by array.
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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.