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opencc-by-4.0Sep 2022View details →

Genome and annotation files (v4_23) for Blumeria graminis f. sp. tritici isolate CHE_96224 (genome assembly: Bgt_genome_v3_16)

Genome and annotation (v4_23) files for Blumeria graminis f. sp. tritici isolate CHE_96224 (genome assembly: Bgt_genome_v3_16)

opencc-zeroAug 2022View details →

Microsatellite profile of Plasmopara viticola isolates collected in Italy

Downy mildew, caused by the oomycete Plasmopara viticola, is one of the most serious threat to viticulture. P. viticola is native to North America and causes the most severe damages to the Eurasian grapevine, Vitis vinifera. In this work, we investigated the genetic structure of the pathogen in Italy by collecting 96 P. viticola strains in twelve different regions. Based on microsatellite characterization (19 microsatellites), we confirmed that the Italian population of P. viticola is composed of two separate subpopulations and determined that these two cluster differ for geographic and climatic conditions. These populations could have been originated from the introduction of two separate populations or, more likely, from the evolution of the original population that reached Europe at the end of the XIX century. The pathogen showed a great evolutionary potential, as highlighted by the regular occurrence of sexual reproduction, panmictic structure within cluster and absence of clones. These results confirm that the P. viticola has a strong potential for adaptation and suggest the integration of all the tools (genetic, agronomic and chemical) for achieving a proper disease management.

opencc-by-4.0Feb 2023View details →

T-cell receptor Vβ (TCRVB) deep sequencing on human T cells isolated from humanized mice engrafted with human PBMC and treated or not with PTCy post-transplantation

Nucleotide sequence data of  TCRVB sequencing performed on T cells isolated from the pre-transplantation hPBMC (donor T cells) or from mice organs at day 21 post-transplantation (injected or not with PTCy at day 3) to determine the impact of PTCy on the T cell V beta (TCRVB) receptor repertoire diversity. NSG mice were engrafted with human PBMC to develop xeno-GVHD and treated or not with 100 mg/kg PTCy. Spleens and lungs from 10 NSG mice per group were pooled and stained to sorted  human CD4+ and CD8+ . DNA of human CD4+ and CD8+ T cells sorted from each organ and  from the PBMC donor was extracted. One hundred fifty µg from each sample were used for T-cell receptor Vβ (TCRVB) deep sequencing performed by Adaptive Biotechnologies.

opencc-zeroSep 2022View details →

Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs

In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (Polygonatum multiflorum (L.) All. and Anemone nemorosa L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1763) and the hoverfly Melanostoma scalare (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.

opencc-by-4.0Apr 2020View details →

Fig. 2 in PREVALENCE OF NOSEMA CERANAE (MICROSPORIDIA) IN THE APIS MELLIFERA MELLIFERA BEE COLONIES FROM LONG TIME ISOLATED APIARIES OF SIBERIA

Fig. 2. Distribution of Nosema species in apiaries throughout the Krasnoyarsk Krai (dots

opencc-zeroOct 2022View details →

Divided by the range: evidence for geographic isolation of the highly mobile Emu (Dromaius novaehollandiae)

Conserving evolutionary processes is becoming increasingly important in conservation management as environmental changes threaten wild populations. Characterising genetically distinct populations and assessing connectivity across the landscape enables wildlife managers to prioritise conservation efforts with limited resources. In the NSW North Coast bioregion of Australia, one of the last remaining coastal populations of the Emu (Dromaius novaehollandiae) has been state-listed as an Endangered Population, owing to its geographic isolation and small census size. Using mitochondrial and nuclear genetic markers, we examined the spatial genetic structure of Emus across south-eastern Australia and assessed the effective population size (Ne) and genetic diversity of the NSW North Coast Emu to inform management. We show significant genetic divergence between the NSW North Coast Emu and other localities based on thousands of highly resolving nuclear markers, which was not explained by geographic distance. Among NSW North Coast Emus, we found less genetic diversity and a critically low effective population size (Ne = 14.84 and 22.49 based on independent methods). Together, these findings suggest that the NSW North Coast Emu is at risk of further losses of genetic diversity and inbreeding depression. Incorporating genetic data into the design of captive-release and translocation projects would refine management plans for this locally important population and monitor risks to its long-term survival.

opencc-by-4.0Sep 2022View details →

Genome assemblies and respective cgMLST profiles of a diverse dataset comprising 1,874 Listeria monocytogenes isolates

Dataset This dataset comprises the genome assemblies and respective 1,748-loci core-genome (cg) Multiple Locus Sequence Type (MLST) profiles [Pasteur schema (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>) available in <a href="https://chewbbaca.online/species/6/schemas/1">chewie-NS</a> (<a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>)]  of a final set of 1,874 Listeria monocytogenes samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the <a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> (NCBI) Sequence Read Archive (SRA) at the beginning of the analysis (November 2021). This set of samples was carefully selected to cover a wide genetic diversity (assessed in terms of Sequence Type [ST]). In total, 204 different STs are represented in this dataset, with ST121, ST6, ST9, ST1 and ST155 being in the top 5 and, together, corresponding to 37.9% of the dataset. File “Lm_metadata.xlsx” contains metadata information for each isolate, including ENA/SRA accession number, BioProject and in-silico MLST ST. The directory “assemblies/” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file.  The file “profiles/Lm_profile.tsv” corresponds to a tab separated file with the 1,748-loci cgMLST profile of each isolate presented in the metadata file. These profiles were determined as explained below.   Dataset selection and curation With the objective of creating a diverse dataset of L. monocytogenes genome assemblies, we collected information about the genetic diversity (STs) of the isolates available at <a href="https://bigsdb.pasteur.fr/listeria/">BIGSdb-Lm</a> database in the beginning of this analysis (November 2021) and in other previous works. Based on this information, we selected an initial dataset comprising 1,957 samples associated with three previous studies (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>; <a href="https://pubmed.ncbi.nlm.nih.gov/28827366/">Maury et al. 2017</a>; <a href="https://pubmed.ncbi.nlm.nih.gov/30775964/">Painset et al. 2019</a>). Their WGS data was downloaded from ENA/SRA with <a href="https://github.com/rpetit3/fastq-dl">fastq-dl</a> v1.0.6. Read quality control, trimming and assembly were performed with the Aquamis v1.3.9 (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145556/">Deneke et al. 2021</a>) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 1,874 isolates passed the dataset curation step and were included in the final dataset. cgMLST profiles of each of these isolates were determined with chewBBACA v2.8.5 (<a href="https://pubmed.ncbi.nlm.nih.gov/29543149/">Silva et al. 2018</a>), using the 1,748-loci Pasteur schema (<a href="https://pubmed.ncbi.nlm.nih.gov/27723724/">Moura et al. 2016</a>) available in <a href="https://chewbbaca.online/species/6/schemas/1">chewie-NS</a> (<a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>) and downloaded on June 23rd, 2022.   Acknowledgements We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.

opencc-by-4.0Apr 2024View details →

SAB_isolates_assembly_annotation

Four organisms were isolated from shelf waters of the South Atlantic Bight; a diatom and coccolithophore from the inner shelf (C. closterium UGA8 and G. oceanica) and the outer shelf (C. closterium UGA4 and G. huxleyi, formerly E. huxleyi). Isolates were grown in steady state high and low iron treatments, with an additional 24hr iron amendment treatment. A hybrid De Novo transcriptome was created with rnaSPAdes for each isolate using Illumina NextSeq and PacBio IsoSeq sequencing. Notebooks associated with this data are on <a title="SAB_isolates" href="https://github.com/CohenLabUGA/SAB_isolates" target="_blank" rel="noopener">GitHub</a>.  Organism codes:  <ul> <li>08 : Inner shelf C. closterium UGA8</li> <li>06: Inner shelf G. oceanica</li> <li>04: Outer shelf C. closterium UGA4</li> <li>13: Outher shelf G. huxleyi</li> </ul> Treatment codes: <ul> <li>pFe19: High Iron</li> <li>pFe21_9: Low Iron</li> <li>add_back: Iron amendment</li> </ul> File descriptions: <ul> <li>transcriptome_assemblies :  zip folder of hybrid assemblies for each isolate using rnaSPAdes</li> <li> <ul> <li>assembly04.fasta - C. closterium UGA4</li> <li>assembly06.fasta - G. oceanica</li> <li>assembly08.fasta - C. closterium UGA8</li> <li>assembly13.fasta - G. huxleyi</li> </ul> </li> <li>predictORFs : zip folder of predicted open reading frames from each assembly using TransDecoder. .pep files are amino acids and .fasta are nucleotide sequences for each predicted ORF  <ul> <li>predict_orfs_04.pep, predict_orfs_04.fasta - C. closterium UGA4</li> <li>predict_orfs_06.pep, predict_orfs_06.fasta - G. oceanica</li> <li>predict_orfs_08.pep, predict_orfs_08.fasta - C. closterium UGA8</li> <li>predict_orfs_13.pep, predict_orfs_13.fasta - G. huxleyi</li> </ul> </li> <li>orf_count : zip folder of salmon quantified predicted open reading frames named by isolate code, treatment, replicate. <ul> <li>C. closterium UGA4: <ul> <li>04add_backA_quant.sf, 04add_backB_quant.sf </li> <li>04pFe21_9A_quant.sf, 04pFe21_9B_quant.sf, 04pFe21_9C_quant.sf</li> </ul> </li> <li>G. oceanica: <ul> <li>06add_backA_quant.sf, 06add_backB_quant.sf, 06add_backC_quant.sf</li> <li>06pFe19A_quant.sf, 06pFe19B_quant.sf, 06pFe19C_quant.sf</li> <li>06pFe21_9A_quant.sf, 06pFe21_9B_quant.sf, 06pFe21_9C_quant.sf    </li> </ul> </li> <li>C. closterium UGA8: <ul> <li>08add_backB_quant.sf, 08add_backC_quant.sf</li> <li>08pFe19A_quant.sf, 08pFe19B_quant.sf, 08pFe19C_quant.sf</li> <li>08pFe21_9A_quant.sf, 08pFe21_9B_quant.sf, 08pFe21_9C_quant.sf</li> </ul> </li> <li>G. huxleyi: <ul> <li>13add_backA_quant.sf, 13add_backB_quant.sf, 13add_backC_quant.sf</li> <li>13pFe19A_quant.sf, 13pFe19B_quant.sf, 13pFe19C_quant.sf</li> <li>13pFe21_9A_quant.sf, 13pFe21_9B_quant.sf, 13pFe21_9C_quant.sf</li> </ul> </li> </ul> </li> <li>annootations : zip folder of eggNOG-mapper functional annotations for each transcriptome <ul> <li>eggnog_anno_04 - C. closterium UGA4</li> <li>eggnog_anno_06 - G. oceanica</li> <li>eggnog_anno_08 - C. closterium UGA8</li> <li>eggnog_anno_13 - G. huxleyi</li> </ul> </li> </ul>

opencc-by-4.0May 2024View details →

Scanning electron microscopy (SEM) images of single bacterial-Pb tolerant isolates

In-Vitro Trace Element Uptake by Bacteria in Liquid Cultures-Scanning Electron Microscopy (SEM-EDX) Analysis Batch studies were conducted using 50 mL Falcon tubes that contained 25 mL GY rich medium supplemented with 100 mg L-1 of Pb (Pb(NO3)2). All tubes were inoculated with 1 mL of a bacterial cell suspension (optical density at 600 nm = 1), which was previously grown in GY medium at 28 °C for 24 h. Samples were incubated at 28 °C and 100 rpm on an orbital shaker. In order to estimate Pb sequestration by bacterial cells, cultures were first centrifuged 15 min at 4800 rpm, bacterial pellets were washed 3 times with 0.01 M phosphate-buffer (PBS, pH 7.0) to remove unbound metals, sugars and proteins. The samples were dehydrated with ethanol/water mixtures, until absolute ethanol. Then 100% acetone was used. Pellets were resuspended in 2% glutaraldehyde for 1h at room temperature. Afterwards, bacterial samples were centrifuged for 3 min at 3000 rpm and pellets were washed 3 times with milli-Q water. One uL of sample was placed on a sample holder, in carbon conductive tape. Then, samples were coated 30 s with a 15 nm gold layer and analysed using a Scanning Electron Microscope (Phenom™ ProX Desktop, Thermofisher). Images were taken using an accelerating voltage of 15 kV. Bacillus paramycoides ST4, Bacillus wiedmannii ST29 and Bacillus proteolyticus ST9 images obtained by SEM-EDX are presented in this dataset. Pb was found present in/on the bacterial cell wall of these bacteria cultures and detected by EDX spectra.

opencc-by-4.0Apr 2024View details →

Twin colony isolate genome assemblies: Chlamydomonas 3112/3222 and WS3/WS7 and Scenedesmus ARA/ARA3

Genomes and assemblies for twin isolate pairs from: David R. Nelson, Amphun Chaiboonchoe, Weiqi Fu, Khaled M. Hazzouri, Ziyuan Huang, Ashish Jaiswal, Sarah Daakour, Alexandra Mystikou, Marc Arnoux, Mehar Sultana, Kourosh Salehi-Ashtiani, Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae, iScience, Volume 11, 2019, Pages 450-465, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2018.12.035. (https://www.sciencedirect.com/science/article/pii/S2589004218302657) Abstract: Summary The activities of microalgae support nutrient cycling that helps to sustain aquatic and terrestrial ecosystems. Most microalgal species, especially those from the subtropics, are genomically uncharacterized. Here we report the isolation and genomic characterization of 22 microalgal species from subtropical coastal regions belonging to multiple clades and three from temperate areas. Halotolerant strains including Halamphora, Dunaliella, Nannochloris, and Chloroidium comprised the majority of these isolates. The subtropical-based microalgae contained arrays of methyltransferase, pyridine nucleotide-disulfide oxidoreductase, abhydrolase, cystathionine synthase, and small-molecule transporter domains present at high relative abundance. We found that genes for sulfate transport, sulfotransferase, and glutathione S-transferase activities were especially abundant in subtropical, coastal microalgal species and halophytic species in general. Our metabolomics analyses indicate lineage- and habitat-specific sets of biomolecules implicated in niche-specific biological processes. This work effectively expands the collection of available microalgal genomes by &sim;50%, and the generated resources provide perspectives for studying halophyte adaptive traits. Keywords: Global Nutrient Cycle; Phycology; Genomics; Metabolomics https://www.sciencedirect.com/science/article/pii/S2589004218302657   Files are as follows:   .fa = assembly .tr.fa = coding sequences .aa.fa = predicted proteins .gff = annotation files

opencc-by-4.0May 2024View details →

Genome sequence resources from three isolates of the apple canker pathogen Neonectria ditissima infecting forest trees

Neonectria ditissima is a generalist ascomycete plant pathogen causing canker diseases on a variety of hardwood tree species and can cross-infect many of them. The fungus enters the plants through wounds throughout the year. N. ditissima is considered a major threat to apple production responsible for the fruit tree canker disease which damages trees and causes rotting of fruits in storage. Nearby forests and shelter belts can serve as source of inoculum for well-managed apple orchards. Thus, knowledge about the N. ditissima isolates infecting different host species is essential for designing integrated pest management strategies. Here, we describe the genomes of three N. ditissima isolates, Nd_iso34, Nd_iso35, and Nd_iso36, infecting European beech, American tulip tree, and American beech, respectively. We obtained genome assemblies of ca. 45 megabases for all isolates, covering 94% of the N. ditissima reference annotation, and 97% of the universal single-copy orthologs (BUSCOs). We conclude that these genome assemblies are a highly relevant resource considering the scarcity of genomic data available for N. ditissima.

Data for isolation-by-environment and its consequences for range shifts with global change: Landscape genomics of the invasive common tansy

Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, U.S.A. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. The dataset includes additional samples from the native range in Finland that were not used in the downstream analysis but are contributed for completeness. The dataset includes the genotype calls for all individuals sampled and sequenced. The genotype file was generated by stacks2.59 running the denovo pipeline and then using the populations function where we kept loci that were in 70% of populations and had a minor allele frequency of at least 1%. We used non-spatial and spatially-explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation-by-distance (IBD) but strong evidence for isolation-by-environment (IBE), indicating that environmental factors may have modulated patterns of range expansion.

Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments

Background Human adenovirus (HAdV) infections are caused by seven mastadenovirus species (A-G) and are the source for a variety of pathologies including gastrointestinal, respiratory, neurological, and ocular disease. While HAdV-D is the most common cause of adenovirus ocular infections, human adenoviruses B and E have also been isolated from the eye. Results In the course of classifying three new atypical ocular adenovirus samples, taken from the vitreous humor, we found that all three isolates were HAdV-B species, with isolate BP-AdV1 sorting with the B1 clade, and isolates BP-AdV2 and BP-AdV3 grouping into the B2 clade. The three Bascom Palmer HAdV-B genomes were then combined with over 300 HAdV-B genome sequences, including 9 ocular HAdV-B genome sequences. The whole genome phylogenetic analysis showed that 9 of the 11 ocular sequences grouped into the B1 clade, forming two clusters within B1. Attempts to categorize the penton, hexon and fiber serotypes using phylogeny of the three Bascom Palmer samples were inconclusive due to incongruence between serotype and phylogeny in the dataset. Recombination analysis using a subset of HAdV-B strains to generate a hybridization network detected recombination between non-human primate and human derived strains, recombination between one HAdV-B strain and the HAdV-E outgroup and limited recombination between the B1 and B2 clades. Conclusions The discordance between serotype and phylogeny detected in this study suggests that the current penton/hexon/fiber-based classification mechanism does not accurately describe the natural history and phylogenetic relationships amongst adenoviruses. A new adenovirus strain classification strategy may be beneficial to the field.

Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China

Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of M. tuberculosis are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in M. tuberculosis. Bedaquiline was found to possess effective antibacterial properties against M. tuberculosis.

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subjected to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12 to 171), the population has been able to maintain high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest underpinning the island adders' ability to maintain a high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

opencc-by-4.0Dec 2023View details →

Figure 1 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 1. Map of geographical locations of research sites.

Crossing data and genomic data for: Strong postmating reproductive isolation in Mimulus section Eunanus

Postmating reproductive isolation can help maintain species boundaries when premating barriers to reproduction are incomplete. The strength and identity of postmating reproductive barriers are highly variable among diverging species, leading to questions about their genetic basis and evolutionary drivers. These questions have been tackled in model systems but are less often addressed with broader phylogenetic resolution. In this study we analyze patterns of genetic divergence alongside direct measures of postmating reproductive barriers in an overlooked group of sympatric species within the model monkeyflower genus, Mimulus. Within this Mimulus brevipes species group, we find substantial divergence among species, including a cryptic genetic lineage. However, rampant gene discordance and ancient signals of introgression suggest a complex history of divergence. In addition, we find multiple strong postmating barriers, including postmating prezygotic isolation, hybrid seed inviability, and hybrid male sterility, leading to complete or substantial postmating isolation in all species pairs. Hybrid seed inviability appears linked to differences in seed size, providing a window into possible developmental mechanisms underlying this reproductive barrier. While geographic proximity and incomplete mating isolation may have allowed gene flow within this group in the distant past, strong postmating reproductive barriers today are likely to prevent any ongoing hybridization. By producing foundational information about reproductive isolation and genomic divergence in this understudied group, we add new diversity and phylogenetic resolution to our understanding of the mechanisms of plant speciation.

opencc-zeroJul 2024View details →

Supplementary data from: A genetic assessment of natural barriers for isolating a proposed Greenback cutthroat trout reintroduction area

We used genetic techniques to evaluate a series of natural waterfalls for their potential to serve as barriers to prevent nonnative salmonids from entering a proposed reintroduction area for federally threatened Greenback cutthroat trout Oncorhynchus clarkii stomias. Genetic samples were collected from nonnative Brook Trout Salvelinus fontinalis at 11 sampling reaches above and below natural waterfalls (height: ~1-3 m under baseflow conditions) along a 33-km segment of Colorado's upper Cache la Poudre River near the outflow of the proposed reintroduction area. To evaluate whether upstream movement of Brook Trout is restricted by any of these waterfalls, we characterized longitudinal trends in genetic diversity along the river corridor and examined patterns of genetic differentiation and population structure in relation to waterfall locations using a panel of microsatellites. We found no evidence that the waterfalls served as complete movement barriers for nonnative Brook Trout based on genetic clustering analyses, estimates of population differentiation, and longitudinal genetic patterns. Our multi-locus assessment did not identify alleles restricted to downstream reaches, and the river segment was genetically homogenized. This evaluation suggests that the existing waterfalls do not fully prevent upstream movement by nonnative Brook Trout, and thus barrier modification would be needed to establish an isolated Greenback cutthroat trout population in the proposed wilderness area.

opencc-by-4.0Jul 2024View details →

Dataset: Assessing Immediate and Lasting Impacts of COVID-19-Induced Isolation on Green Space Usage Patterns

It includes the data for paper "Assessing Immediate and Lasting Impacts of COVID-19-Induced Isolation on Green Space Usage Patterns".