Find research datasets worth reusing

opencc-by-4.0May 2023View details →

A genome-wide genetic screen uncovers novel determinants of human pigmentation

1717.gwas.imputed_v3.both_sexes.variants.nolowconf.maf01.clumped.txt - GWAS results for LD-clumped genome-wide significant variants from White British skin color GWAS 1717.gwas.imputed_v3.both_sexes.variants.nolowconf.maf01.pbsfilt.100kb.tsv - GWAS results for LD-pruned variants within 100kb of pro-melanin genes eqtl.gwas.minpergene.txt - melanocyte eQTL and White British skin color GWAS results for SNPs near pro-melanin gene. Columns 1-12 are eQTL info, 13 onwards are GWAS info. Select rows with "closest" = TRUE and both p-values < 0.01 to recreate figure in the paper. csv_and_r_script_files.tar- csv and R script files to recreate the figures in the paper.  PBS_Pigmentation.tar- txt and R script files to recreate PBS figures in the Figure

FIGURE 7 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 7. Amendments to Clades 2 and 4 of the phylogeny of Calderón-Acevedo et al. (2022). Alphanumeric codes to the left of the equal signs are those used by these authors to label their samples (Aaeq = A. aequatoris; Acar = A. carishina; Acau = Anoura caudifer; Ageo = A. geoffroyi; Alat = A. latidens; Alui = A. luismanueli; and Aperu = A. peruana). Acronyms to the right of the equal signs are those of the museums in which the specimens are housed, except for JFD which are the collector's initials. These acronyms are followed by catalog or field numbers. Bold type indicates specimens whose taxonomic identifications are being challenged. Asterisks indicate specimens examined by JM. The species names to the right of brackets indicate the taxonomic identities assumed in our study. In the original tree (Calderón-Acevedo et al., 2022), all specimens in Clade 2 were deemed to be A. caudifer, and all specimens in the A. geoffroyi-A. peruana subclade of Clade 4 were deemed to be A. geoffroyi.

FIGURE 5 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 5. Maps of SE Central America and NW South America showing in gray present and past abiotically suitable areas for Anoura cultrata, as predicted by ecological niche modeling analyses. Darker shades of gray indicate stronger model support. Filled circles represent records for the species. Climatic scenarios are: top left, present climatic conditions; top right, HCO, Holocene Climatic Optimum; bottom left, LGM, Last Glacial Maximum; bottom right, LIG, Last Interglacial.

FIGURE 4 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 4. Relative position of six geographic groups and 122 specimens of Anoura cultrata in the space defined by a Linear Discriminant Analysis (LDA) of the 7 wing and 14 cranial measurements considered in the study. Specimen scores obtained by means of the second, third, and fourth discriminant functions (DF2, DF3, DF4) were plotted against those obtained by means of the first (DF1). The percentage of variance accounted by each of the four axes is indicated in their legends. COPA, Costa Rica–W Panama (empty triangles); EPA, E Panama (filled triangles); NVE, N Venezuela (filled diamonds); WVE, W Venezuela (empty diamonds); COEC, Colombia–Ecuador (filled circles); PEBO, Peru–Bolivia (empty squares). Eigenvalues and variable loadings are provided in Supplementary Information S1.

FIGURE 3 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 3. Box-and-whisker plots comparing the wing and cranial sizes of six geographic groups of Anoura cultrata: COPA, Costa Rica–W Panama; EPA, E Panama; NVE, N Venezuela; WVE, W Venezuela; COEC, Colombia–Ecuador; and PEBO, Peru–Bolivia. The height of each gray box represents the interquartile range (IQR), containing 50% of data points. Within each box, the horizontal line represents the median, and the empty square the mean. The upper and lower 'whiskers' respectively indicate the distance from the box of the largest value within Q3 + 1.5 × IQR, and the smallest value within Q1 - 1.5 × IQR. The numbers on the top of upper 'whiskers' indicate the sample sizes. The distribution of the values on which each plot is based is shown to its left. Values above the upper 'whisker' and below the lower 'whisker' are considered outliers. Scores on the first axes (PC1) of Principal Components Analyses were used as proxies of wing (6 measurements, forearm length excluded) and cranial (13 measurements, skull length excluded) sizes. The PC1 of wing measurements accounts for 57.19 %, and the PC1 of cranial measurements for 58.36 % of variance. Eigenvalues and variable loadings for the two PCAs are provided in Supplementary Information S1.

FIGURE 1 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 1. Craniodental measurements used in morphometric analyses. The dorsal, lateral, and ventral views of the cranium, and lateral view of the mandible correspond to a male specimen of Anoura cultrata (MCNG 1035) from Venezuela (Merida Cordillera). Abbreviations are: BB, breadth of braincase; BH, braincase height; CBL, condylobasal length; C–C breadth; C–M3 length; c–m3 length; GLS, greatest length of skull; LM, length of mandible; M3–M3 breadth; MB, mastoid breadth; PL, palatal length; PC, postorbital constriction; RB, rostrum breadth; and ZB, zygomatic breadth.

FIGURE 2 in Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

FIGURE 2. Mountain systems of SE Central America and NW South America in which Anoura cultrata has been recorded (filled circles). Elevations above 500 m are indicated in light grey. Elevations above 2,000 m are indicated in dark grey. Abbreviations for mountain systems are: CC, Venezuelan Coast Range [Cordillera de la Costa]; CCE, Colombian Central Cordillera [Cordillera Central de Colombia]; CM, Merida Cordillera [Cordillera de Mérida]; COC, Colombian Western Cordillera [Cordillera Occidental de Colombia]; COR, Colombian Eastern Cordillera [Cordillera Oriental de Colombia]; CP, Putumayo corridor [Corredor de Putumayo]; CVF, Chorotega Volcanic Front [Frente Volcánico de Chorotega]; DAH, Darien Highlands [montañas del Darién]; GH, Guiana Highlands [Macizo (or Escudo) Guayanés]; MT, Turimiquire Massif [Macizo de Turimiquire]; PA, Azuero Peninsula Highlands [montañas de la Península de Azuero]; SB, Baudo Mountains [Serranía del Baudó]; SNSM, Santa Marta Mountain Range [Sierra Nevada de Santa Marta]; SP, Perija Mountain Range [Serranía (or Sierra) de Perijá]. Abbreviations for depressions [highlighted in bold in the map] separating mountain systems are: C, Cauca Valley [Valle del Cauca]; CPL, Central Panamanian Lowlands [Tierras Bajas Centrales de Panamá]; DASJ, Atrato–San Juan Depression [Depresión del Atrato–San Juan]; DH, Huancabamba Depression [Depresión de Huancabamba]; DL, Lara Depression [Depresión de Lara]; DN, Nicaragua Depression [Depresión de Nicaragua]; DT, Tachira Depression [Depresión del Táchira]; DU, Unare Depression [Depresión de Unare]; DY, Yaracuy Depression [Depresión de Yaracuy]; M, Magdalena Valley [Valle del Magdalena]; PA, Andalucia pass [Paso de Andalucía]; VSP, Suaza-Pescado valleys [Valles de Suaza-Pescado].

FIGURE 3. A in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 3. A) Maximum Likelihood phylogram and B) SVD Quartets cladogram of relationships among Mixophyes based on Single Nucleotide Polymorphisms. Alphanumeric codes refer to collection location details and ABTC numbers in Table 1.

FIGURE 6 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 6. Cross bar patterns on hindlimbs of Mixophyes. Side by side comparison of A) thigh and B) tibia-fibula in life of left Mixophyes balbus from Coombadjha Creek Washpool NP and right M. australis sp. nov. from Congewai Creek, Watagan NP. Thighs of Mixophyes balbus from C) Little Styx River, New England NP, D) Thungutti Creek, New England NP, E) Coombadjha Creek, Washpool NP, and Mixophyes australis sp. nov. from F) Congewai Creek, Watagan NP, G) Frying Pan Creek, Chichester SF and H) Sharpes Creek, Gloucester Tops NP.

FIGURE 5 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 5. Plots of linear discriminants for analyses of morphological variation among Mixophyes balbus (blue) and Mixophyes australis sp. nov. (red).

FIGURE 7 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 7. Mixophyes balbus in life. A) Rockadooie Ck, Curramore SF, Michael Mahony, B) Coombadjha Ck, Washpool NP, Stephen Mahony, C) Washpool NP, Gibraltar Range, Stephen Mahony, D) Coombadjha Ck, Washpool NP, Stephen Mahony, E) Forestland SF, Stephen Mahony, F) Forestland SF, Stephen Mahony.

FIGURE 10 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 10. Comparison of geographic pattern of relationships among mitochondrial DNA sequences and nuclear genetic (SNP) groups, highlighting the discordance in relationships among samples inferred from the two genomic compartments. Refer to Table 1 for locality code information and ABTC numbers.

FIGURE 4 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 4. Single Nucleotide Polymorphism Principal Component Analysis of Mixophyes fleayi and M. balbus. A) PC1 v PC2, B) PC3 v PC4, C) STRUCTURE barplot of all ingroup samples, D) STRUCTURE barplot of southern group samples only.

FIGURE 2 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 2. Bayesian phylogram of relationships among mitochondrial ND2 haplotypes in Mixophyes. Values at nodes represent ML bootstrap proportions (left) and Bayesian posterior probabilities (right). The tree was rooted with sequences from the outgroups and Lechriodus melanopyga, Limnodynastes salmini and Neobatrachus pictus (Table 1). Alphanumeric codes refer to collection location details and ABTC numbers in Table 1.

FIGURE 8 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 8. Mixophyes australis sp. nov. in life. A) Holotype AMS R188750, Sharpes Creek, Gloucester Top NP, Ross Knowles, B) Sharpes Creek, Gloucester Top NP, C) Gap Creek, Watagan NP, Stephen Mahony, D) Abbots Ck, Olney SF, Stephen Mahony, E) Cockerawombeeba Ck, Hastings Range, Michael Mahony, F) Cockerawombeeba Ck, Hastings Range, Michael Mahony.

FIGURE 1 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 1. Map showing collection locations sampled for molecular genetic analysis of Mixophyes in eastern Australia. Alphanumeric codes refer to collection location details in Table 1. Small black dots are voucher records from the Atlas of Living Australia, yellow triangles—M. fleayi, blue circles—M. balbus northern group, red squares—M. balbus southern group.

FIGURE 9 in A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses

FIGURE 9. Reproductive calls of Mixophyes balbus and Mixophyes australis sp. nov. A) Oscillogram and spectrogram of a series of advertisement calls and encounter calls of Mixophyes australis sp. nov. over 40 seconds duration, B) a single call with the time axis expanded (1.5 seconds duration), C) oscillogram and spectrogram of a series of advertisement calls and encounter calls of Mixophyes balbus over 40 seconds duration, D) a single call with the time axis expanded (1.5 seconds duration), E) oscillogram and spectrogram of an encounter call of Mixophyes australis sp. nov., (0.4 second time axis), and F) oscillogram and spectrogram of an encounter call Mixophyes balbus (0.4 second time axis). a = advertisement call, e = encounter call, and kHz is kilohertz.

Fig. 6 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 6. Haplotype network of Leucotaraxis piniperda DNA barcode sequences.The area of each pie chart is proportional to the number of samples sharing that haplotype. Small black dots represent unsampled haplotypes. Pie charts indicate the proportions of flies sampled from different host plant genera of adelgid prey.

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 microsatellite loci.The height of each bar represents the proportion of an individual′s genotype assigned to each of K = 4 clusters.The names of the clusters correspond to those in Fig. 1C. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 microsatellite loci. The height of each bar represents the proportion of an individual′s genotype assigned to: A) each of K = 2 clusters for analysis of all individuals, and B) each of K = 2 clusters for analysis of only western individuals.The names of the clusters correspond to those in Fig. 1D. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.