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423 results for “Haplotypes”

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One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one‐locus‐several‐primer‐sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey–predator interactions.

opencc-zeroDec 2018View details →

zenodo40/100

Fig. 11 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 11. Haplotype network of Ngirhaphium sivasothii. Thailand: Krabi, Phangnga, Satun; Singapore: Sarimbun, Pulau Tekong, Pulau Ubin, Labrador, Semakau Island, and Sungei Buloh.

opencc-by-4.0Nov 2019View details →

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Fig. 10 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 10. Haplotype network of Ngirhaphium murphyi. Singapore: Pulau Ubin, Mandai Sungei Buloh; Thailand: Satun and Krabi.

opencc-by-4.0Nov 2019View details →

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Fig. 12 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 12. Compilation of male terminalia of Ngirhaphium in lateral view. A, Ngirhaphium sivasothii left side with ventral surstylus removed; cerci dorsally; B, Ngirhaphium murphyi left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; C, Ngirhaphium caeruleum left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; D, Ngirhaphium meieri, new species left side with ventral surstylus removed; E, Ngirhaphium chutamasae left side with ventral surstylus removed; F, Ngirhaphium thaicum, new species right side. Scale = 0.1 mm.

opencc-by-4.0Nov 2019View details →

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Fig. 8 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 8. Ngirhaphium meieri, new species, holotype male terminalia: A, Lateral view of genital capsule with left ventral surstylus removed; B, Cerci dorsally; C. Left ventral surstylus; D, Ventral view of genital capsule. Abbreviations: ae = aedeagus; c = cercus; ds = dorsal surstylus; hy = hypandrium; sp = sperm pump; vs = ventral surstylus. Scale = 0.1 mm.

opencc-by-4.0Nov 2019View details →

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Fig. 5 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 5. Ngirhaphium thaicum, new species male terminalia (27_009) A, epandrium left side; B, cerci dorsal view; C, left surstylus inside view. Scale = 0.1 mm.

opencc-by-4.0Nov 2019View details →

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Fig. 2 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 2. Ngirhaphium caeruleum-complex. View of inside of the dorsal surstylus of the left side and the fused dorsal and ventral surstyli of the right side. Scale = 0.1mm. A, green caeruleum from Tutong, Brunei (ZRCBDP0066395) at 1.6 % from the Semakau population; B, green caeruleum from Pulau Tekong, Singapore (ZRCBDP0001462) at 0.6% from the Semakau population; C, green caeruleum from Pulau Ubin, Singapore (ZRC_BDP_0084430) at 0.6% from the Semakau population; D, blue caeruleum from the type locality on Semakau Island, Singapore (ZRCBDP0118762); E, green thaicum, new species from Surat Thani, Thailand (24-018) at 4.2% from the Semakau population; F, green thaicum, new species from Cambodia (JP3C_Ngi-cambodiensis_Misc002) within the variability of the southern Thailand populations.

opencc-by-4.0Nov 2019View details →

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Fig. 1 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 1. Haplotype network of the Ngirhaphium caeruleum-complex. Brunei: Berambang, Tutong, Labu; Singapore: Pulau Ubin, Pulau Tekong, Semakau Island; Thailand: Chumphon, Surat Thani, and Cambodia.

opencc-by-4.0Nov 2019View details →

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Fig 4. Median-joining haplotype network for M in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences

Fig 4. Median-joining haplotype network for M. fascicularis. The size of the circular nodes representing haplotypes is proportional to the number of sequences comprising the haplotype. Shading of circular nodes corresponds to general geographic groupings including Sundaic islands (white), mainland Indochina (gray), Malay Peninsula and northern Sumatra (dark gray), and Singapore (black). Haplotype identifications are presented in Table 1.

opencc-by-4.0Feb 2017View details →

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FIGURE 3. Haplotype network inferred from A in On the taxonomic identity of Pteronotus davyi incae Smith, 1972 (Chiroptera: Mormoopidae)

FIGURE 3. Haplotype network inferred from A, cyt-b and B, CO1 datasets, highlighting the clusters corresponding to Pteronotus davyi, P. fulvus, and P. gymnonotus. Each circle represents one distinct haplotype (H), whose size is proportional to its frequency in the sample (1 to 6 individuals).

opencc-by-4.0Mar 2021View details →

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Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D in Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA

Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D. Posterior probability values ≥ 90% are shown. Upper Sacramento River basin lineages newly discovered in this study are highlighted by the larger font. Specimen codes are from Table 1.

opencc-by-4.0Mar 2007View details →

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Figure 4. Statistical haplotype networks for COI, 16S in Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: Theodoxus )

Figure 4. Statistical haplotype networks for COI, 16S and ATPα sequence data for Pontocaspian and southern Iranian Theodoxus groups. The total number of sequences in each network is demarcated by 'n'. The circle sizes represent the relative frequency of sequences per haplotype. The number of site changes separating haplotypes is indicated by blank dots. Colours correspond to the sampling locations, as indicated in the key and in figure 2. Haplotype groupings are boxed and labelled according to the phylogroups determined through the dated phylogeny (I–VI; figure 3).

opencc-by-4.0Oct 2019View details →

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Haplotype analysis of GWAS candidates identified for root:shoot ratio changes under salt stress in Arabidopsis

The haplotype analysis was performed on 7 loci identified through GWAS by Magdalena Julkowska, while she was a PostDoc at KAUST, Saudi Arabia, workin in the lab of Dr. Mark Tester.

opencc-by-4.0Nov 2022View details →

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Figure 4. Haplotype network for Rattus rattus Complex II in Expanding Population Edge Craniometrics and Genetics Provide Insights into Dispersal of Commensal Rats through Nusa Tenggara, Indonesia

Figure 4. Haplotype network for Rattus rattus Complex II. The Nusa Tenggara samples are illustrated on the right of the network.

opencc-by-4.0Nov 2020View details →

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Figure 3. Haplotype networks for Rattus exulans, R in Expanding Population Edge Craniometrics and Genetics Provide Insights into Dispersal of Commensal Rats through Nusa Tenggara, Indonesia

Figure 3. Haplotype networks for Rattus exulans, R. argentiventer, and Rattus rattus Complex LIV. Sunda refers to the islands of Borneo, Java, and Sumatra; the Indonesian sample (brown) lacks further collection information.

opencc-by-4.0Nov 2020View details →

zenodo40/100

Haplotype-aware reference genome reveals hidden somatic mutations of sweet orange

Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).   Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Filename: ASE_in_five_fruit_development.txt Description: Based on our haplotype sequences, we confirmed biallelic genes showed significant expression difference between two alleles in at least one fruit developmental stage. We collected the RNA-seq data from fruit of Newhall navel orange at five developmental stages (90, 120, 150, 180 and 210 days after bloom). RNA-seq data from previous project GSE108930 in NCBI database.   Filename: Biallelic_genes_haplogenomes.tsv Description: The biallelic genes were identified using the Genespace program.   Filename: Haplogenomes_CENH3_chip_peaks.bw Description: The CENH3 sequences were collected from BankIt ID 2305947. These reads (including the input library as a control) were aligned to the two assembled haplotypes using Bowtie2 (v2.5.1) with default parameters. MACS2 (v2.2.7.1) with the additional parameters “-f BAM -ghs -B -q 0.01” was used to perform peak calling. The peaks generated from CENH3 chip-seq.   Filename: Haplogenomes_Control_chip_peaks.bw Description: The peaks generated from Control chip-seq.   Filename: Haplotype_based_79accessions_somatic_variations.vcf Description: The small somatic variations generated based on the haplotype-based method. The derived somatic mutations were identified based on nine samples from the outgroup (Earlier Clade I).   Filename: HaplotypeA_CuteSV.vcf Description: The HiFi reads were mapped to haplotype A. We called SVs using the CuteSV program.   Filename: HaplotypeA_gene_function_annotation.tsv Description: The gene annotations of haplotype A.   Filename: HaplotypeA_gene_model.gff3 Description: The gene structure model of haplotype A.   Filename: HaplotypeA_genome.fa Description: The genome sequences of haplotype A.   Filename: HaplotypeA_PEPPER_OUTPUT.zip Description: The small variations of sweet orange using the haplotype A as the reference genome.   Filename: HaplotypeA_TEs_annotation.gff3 Description: The TE annotations of haplotype A.   Filename: HaplotypeB_gene_function_annotation.tsv Description: The gene annotations of haplotype B.   Filename: HaplotypeB_gene_model.gff3 Description: The gene structure model of haplotype B.   Filename: HaplotypeB_genome.fa Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material). Description: The genome sequences of haplotype B.   Filename: HaplotypeB_TEs_annotation.gff3 Description: The TE annotations of haplotype B.   Filename: Single_reference_87accessions_somatic_variations.vcf Description: The small somatic variations generated based on the single reference genome (Haplotype A).   Filename: Somatic_material_RNA_seq_matrix.txt Description: The expression matrix of BT_3 and BT_5 (a set of somatic mutation material).

opencc-by-4.0Nov 2023View details →

dryad40/100

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

Open the record for dataset details and reuse information.

publicJul 2023View details →

dryad36/100

Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

opencc-zeroAug 2020View details →

dryad36/100

Color scores, COI haplotypes and SNP data for Phelotrupes auratus individuals

We studied the population genetic structure underlying the geographic variation in the structural color of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colors of different reflectance wavelengths perceived as red, green, and indigo. These forms occur parapatrically in an area of Japan. The color variation was not related to variation in climatic factors. Using single-nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red, and east/red) by a combination of genetic clusters (west, south, and east) and three color forms. There were three transition zones for the color forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colors. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident color changes, which implies regionally specific selection on the different colors. In a genome-wide association study, we identified four SNPs that were associated with the red/green or indigo color and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different color range. These loci may have controlled the transitions between different combinations of colors. Our study demonstrates that geographic color variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colors, and the effects of different color loci.

opencc-zeroNov 2020View details →

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Contrasting association of Leptin receptor polymorphisms and haplotypes with polycystic ovary syndrome in Bahraini and Tunisian women: a case–control study

Background. This study examined the contribution of ethnicity to the association of leptin receptor gene (LEPR) genetic variants with polycystic ovary syndrome (PCOS) in Tunisian and Bahraini Arabic-speaking women. Methods. Subjects consisted of 320 women with PCOS, and 446 eumenorrhic women from Tunisia, and 242 women with PCOS and 238 controls from Bahrain. Genotyping of (exonic) rs1137100 and rs1137101 and (intronic) rs2025804 LEPR variants was done by allelic exclusion. Results. The minor allele frequencies of rs1137100 and rs1137101 were significantly different between PCOS cases and control women from Bahrain but not Tunisia, and LEPR rs1137101 was associated with increased PCOS susceptibility only in Bahraini subjects. Furthermore, rs1137100 was associated with decreased PCOS risk among Bahrainis under codominant and recessive models; rs1137100 was negatively associated with PCOS in Tunisians after controlling for testosterone. In addition, rs2025804 was associated with increased PCOS risk among Tunisian but not Bahraini women, after adjusting for key covariates. Negative correlation was seen between rs1137101 and triglycerides in Tunisians, while HOMA-IR and insulin correlated with rs2025804 and rs1137101 among Bahraini subjects, and rs1137101 correlated with estradiol and prolactin. Taking TAG haplotype as common, positive association of TAA and negative association of TGG haplotype with PCOS was seen among Bahraini women; no three-locus PCOS-associated haplotypes were found in Tunisians. Conclusions. This study is the first to demonstrate the contribution of ethnicity to the association of LEPR gene variants with PCOS, thereby highlighting the significance of controlling for ethnicity in gene association investigations.

opencc-zeroDec 2020View details →

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Allen Brain Atlas

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neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

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Last verified 2026-04-30Open record

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.

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electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

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behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record