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Figure S3 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

Figure S3. Scaled residuals from the fit of the model to the data. Allowing eight migration events 98.6% of the variance in relatedness between taxa was explained by the tree. Colours are described in the palette on the right.

FIGURE 3 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

FIGURE 3 | (A) Maximum Likelihood (ML)-tree inferred by TreeMix allowing eight migration events. Letters A–H refer to migration edges as defined in Table 1. Migration H, not confirmed by the f4 statistic after the Holm-Bonferroni correction (see Table 3), is shown using a two-dashed line. Migration arrows are colored according to their weight and colors are explained in the palette on the left. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Drift parameter is shown on the x-axis.

FIGURE 2 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

FIGURE 2 | (A) The Maximum Likelihood (ML)-tree inferred by TreeMix under the strictly bifurcating model. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Drift parameter is shown on the x-axis. (B) Scaled residuals from the fit of the model to the data. Without migration events 91.7% of the variance in relatedness between taxa was explained by the tree. Colors are described in the palette on the right.

Figure S1 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

Figure S1: The decay of linkage disequilibrium (LD) in: V. acerifolia, V. aestivalis, V. aestivalis var. aestivalis, V. champinii, V. cinerea, V. cinerea var. helleri, V. labrusca, V. riparia, V. rupestris, V. vinifera subsp. vinifera, V. vulpina. LD was estimated calculating the pairwise squared correlation based on genotypic allele counts (--r2 option in PLINK; Purcell et al. 2007) for all intrachromosomal SNP loci up to 500 kb. Each point represents the median r2 value and the mean physical distance from bins of 75 pairwise SNP comparisons. LD decay is rapid in all species considered. N: the number of individuals sampled to estimate LD; Bin width: the number of pairwise r2 values included in each bin; dotted black lines indicate r2= 0.2. Physical inter-marker distance is expressed as kilobase pairs (kb).

FIG. 3 in Phylogeny and biogeography of wild roses with specific attention to polyploids

FIG. 3. Network representing the relationships among copies of GAPDH obtained from Rosa species. A 'c' followed by a number indicates the number attributed to one particular clone sequenced. The groups are compared with our main clades from the chloroplast analyses. Purple is attributed to Rosa subgen. Platyrhodon, yellow to R. sect. Banksianae, bright orange to R. sect. Bracteatae, brown to R. sect. Laevigatae, light pink to Pimpinellifoliae clade, green to Cinnamomeae clade, light blue to Synstylae clade and a deeper blue to R. sect. Caninae. Two species have a particular colour, R. spinosissima is highlighted with a deeper pink colour and R. abyssinica with a light orange colour. Two types of copies, C1 and C2, are distinguished in our Cinnamomeae group. Some polyploids have several copies with different affinities. The names of known polyploids are in bold (in R. sect. Caninae all species are presumed to be polyploids even when the ploidy number is not exactly known).

FIG. 4 in Phylogeny and biogeography of wild roses with specific attention to polyploids

FIG. 4. Chronogram obtained from BEAST analyses of chloroplast regions. Branches are coloured according to the ancestral area reconstruction analyses (DEC model) including fossils information. A P designates our Pimpinellifoliae clade, a C our Cinnamomeae clade and an S our Synstylae clade. The names of known polyploids are in bold (in R. sect. Caninae all species are presumed to be polyploids even when the ploidy number is not exactly known).

FIGURE 1 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

FIGURE 1 | (A) Linkage disequilibrium (LD) decay in ten grape species. The median r2 calculated in bins of 75 pairwise SNP comparisons was plotted against the mean physical distance of each bin (kb). Sample size for each species is shown in figure. Dotted line indicates r2 = 0.2. (B) Multistep procedure followed to identify the appropriate SNP block size used in TreeMix analysis. The SNP block size tested at each step is shown above plots. The physical distance (kb) between midpoints of consecutive blocks placed on the same chromosome is shown on y-axis while the x-axis shows the number of pairwise distances computed at each step. The dashed red line represents the assumed distance threshold (i.e., 200 kb).

FIG. 1 in Phylogeny and biogeography of wild roses with specific attention to polyploids

FIG. 1. Morphological diversity of flowers and fruits of a few representatives of Rosa. (A) Flower of Rosa hugonis. (B) Flower of R. moyesii. (C) Flower of R. multibracteata. (D) Flower of R. odorata. (E) Flower of R. praelucens. (F) Flower of R. prattii. (G) Flower of R. tsinglingensis. (H) Flower of R. roxburghii. (I) Flower of R. rubus. (J) Flower of R. roxburghii. (K) Flower of R. villosa. (L) Flower of R. primula. (M) Fruit of R. sikangensis. (N) Fruits of R. omeiensis. (O) Fruit of R. mairei. (P) Fruit of R. macrophylla. (Q) Fruits of R. sweginzowii.

FIGURE 4 in Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

FIGURE 4 | The figure shows the phylogenetic relationships of grapes referred to this work. Linking lines between corresponding tips are used to highlight changes in tree topology and taxa placements due to the addition of migration events. Left: the strict consensus tree between the two the best-scoring Maximum Likelihood (ML) tree topology obtained from 400 ML searches performed by TreeMix under the strictly bifurcating model. Right: strict consensus tree of the forty ML trees inferred by TreeMix allowing nine migration events. Bootstrap values (500 replicates) are shown for each node.

FIG. 2 in Phylogeny and biogeography of wild roses with specific attention to polyploids

FIG. 2. Phylogenetic relationships among Rosa species as reconstructed by Maximum Likelihood analyses of three chloroplast regions (psbA-trnH spacer, trnL region and trnG region). Bootstrap values are placed as close as possible to the node supported. The ploidy level of each species is given after its name (see Erlanson, 1929, 1934, 1938; Roberts, 1977; Yokoya et al., 2000; Roberts et al., 2009; Jian et al., 2010). The names of known polyploids are in bold (in R. sect. Caninae all species are presumed to be polyploids even when the ploidy number is not exactly known). Wissemann's (2003) classification is compared with our clades. A P designates our Pimpinellifoliae clade, a C our Cinnamomeae clade, an S our Synstylae clade, Ca our Caninae clade and Ru our Rubiginae clade.

opencc-zeroMay 2023View details →

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Challenges of copro-parasitological surveys in wild Iberian ibex (Capra pyrenaica) populations addressed through a combination of molecular and statistical tools

Copro-parasitological surveys in wildlife face challenges due to the secretive nature of many species and the unknown performance of the diagnostic tests employed. To overcome these issues, we used a combination of hierarchical models (site-occupancy and N-mixture models) applied to copro-parasitological data obtained from faecal samples assigned to the host species by molecular methods in the Iberian ibex in north-western Iberian Peninsula. The aims were to compare the performance of four diagnostic tests (Mini-FLOTAC, McMaster, Willis flotation, and natural sedimentation) and to use this methodological approach (molecular analysis with hierarchical models) to better estimate positivity proportion and shedding intensity in a wild ibex population. Pooled faecal samples were collected, and those confirmed by molecular analyses to be the host species in question were included in the study. Hierarchical models confirmed different performances of each diagnostic test, with Mini-FLOTAC showing higher sensitivity for eimeriid coccidia, Willis flotation (for proportion positive) and McMaster (for shedding intensity) in gastrointestinal Strongylida, and equal performance of MiniFlotac/Willis flotation (for proportion positive) and MiniFlotac/McMaster (for shedding intensity) in Moniezia spp. This study employed a combination of molecular and statistical methods that improved the estimates of prevalence and shedding intensity and allowed us to compare the performance of four diagnostic tests while assessing the effect of covariates. Such improvements are critical to enhancing inference in non-invasive wildlife copro-parasitological studies.

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Reproductive asynchrony within social groups of female eastern wild turkeys

Coordination in timing of reproduction is driven by multiple ecological and sociobiological processes for a wide array of species. Eastern wild turkeys (Meleagris gallopavo silvestris) use a male dominance polygynous mating system, where males communicate with females via elaborate courtship displays and vocalizations at display sites. Most females prefer to mate with dominant males, therefore asynchronous breeding and nesting may occur which can disproportionately influence individual fitness within breeding groups. For female wild turkeys, there are reproductive advantages associated with earlier nesting. As such, we evaluated reproductive synchrony within and between groups of GPS-tagged female eastern wild turkeys based on timing of nest initiation. We examined 30 social groups with an average of 7 females per group (range 2-15) during 2014-2019 in west central Louisiana. We found that the estimated number of days between first nest initiation across females within groups varied between 3-7 days across years, although we expected 1-2 days to occur between successive nesting attempts of females within groups based on observations of captive wild turkeys in the extant literature. The number of days between successive nest attempts across females within groups was lower for successful than failed attempts, and nests with an average of 2.8 days between initiation of another nest were more likely to hatch. Our findings suggest that asynchronous reproduction may influence reproductive success in female wild turkeys.

opencc-zeroMay 2023View details →

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Data from: Dispersal-induced social stress prolongs gestation in wild meerkats

In the majority of mammals, gestation length is relatively consistent and seldom varies by more than 3%. In a few species, females can adjust gestation length by delaying the development of the embryo after implantation. Delays in embryonic development allow females to defer the rising energetic costs of gestation when conditions are unfavourable, reducing the risk of embryo loss. Dispersal in mammals that breed cooperatively is a period when food intake is likely to be suppressed and stress levels are likely to be high. Here we show that pregnant dispersing meerkats (Suricata suricatta), which have been aggressively evicted from their natal group and experience weight loss and extended periods of social stress, prolong their gestation by means of delayed embryonic development. Repeated ultrasound scans of wild, unanaesthetised females throughout their pregnancies showed that pregnancies of dispersers were on average 6.3% longer and more variable in length (52-65 days) than those of residents (54-56 days). The variation in dispersers shows that, unlike most mammals, meerkats can adapt to stress by adjusting their pregnancy length by up to 25%. By doing so, they potentially rearrange the costs of gestation during adverse conditions of dispersal and enhance offspring survival.

opencc-zeroJun 2023View details →

Fig. 2 A in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 2 A Manhattan plot of the V. arizonica genome showing markers associated with bacterial load. The plot denotes each of the 19 chromosomes for haplotype 1. Each circle represents a SNP with a corresponding p value, based on EMMAX genome-wide association analysis. The 25 SNPs that were detected in two separate GWA analyses are circled in red and define the 8 peaks of association, which are numbered as P1, P2, etc., and referred to in the text. In addition to SNPs, the locations of significantly associated kmers and CNVs are provided when they overlap with a SNP-defined peak. The colored horizontal lines represent the cut-off p-values (P <0.05, Bonferroni corrected) for the different marker types. Significant (P <0.05, Bonferroni corrected) kmers and CNVs are represented by red and blue triangles, respectively.

Fig. 1 Vitis arizonica sampling and phenotypes. A in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 1 Vitis arizonica sampling and phenotypes. A map of the Southwestern United States and Northern Mexico indicates sampling locations of the n = 167 V. arizonica accessions used in this study. The color of sample locations (circles) are colored according to their resistance phenotype, as measured by bacterial load (CFU/mL). The histogram of phenotypes (in CFU/mL) is to the right of the map. Map generation relied on information from GADM, a publicly available database (http:gadm.org).

Fig. 5 in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 5 Relationships among resistance, genetic markers and bioclimatic data. a The estimated relative importance, from GF modeling, of each of the bioclimatic variables tested. The y-axis is a measure of the importance of various variables to explain the model - i.e., the relative importance of each bioclimatic variable for predicting changes in allele frequency across the landscape. Each boxplot denotes the average inferred importance of the bioclimatic variable, with the whiskers plotting the standard deviation of 1000 separate analyses (gray dots). BIO8 was estimated to have the biggest impact on the model in all 1000 analyses. b The turnover function showing the temperature range of BIO8 on the x-axis and the change in the genetic composition on the y-axis. The circles represent individuals that are colored by resistance (gray) or susceptible (white). c Individual predictors in a linear model to predict resistance levels (CFU/ml). The label score_ref represents sets of 1000 randomly chosen sets of 25 SNPs; K1 and K2 are the proportion of the assignments to each admixture group for each individual. The other predictors include bioclimatic variables and genomic data, as listed in the text, each evaluated 1000 times with bootstrapped datasets. Each boxplot reports the second and third quartiles, with median values in the square and circles showing outliers. The barplot whiskers report standard deviation, and the dashed horizontal line reflects the median value of 1000 replicates of the Rpd score. d The density distribution of BIO8 for a global database of locations of Xylella fastidiosa detection.

Fig. 4 in Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Fig. 4 The presence of resistance and susceptibility kmers in different data sets. a Analyses within the V. arizonica sample set. The top-left graph indicates the 99 different resistance (R-kmers) kmers across the x-axis, with their detection frequency across the resistant (CFU/mL <13) accessions. The top-right graph plots the average detection frequency of susceptibility kmers (S-kmers). The bottom-left and bottom-right graph are similar, they but show R-kmer and S-kmer detection frequencies among susceptible accessions. b The same graphs as in A, but the top graphs plot R-kmer and S-kmer detection frequencies for the five V. vinifera cultivars bred for PD resistance by backcrossing to V arizonica, while the bottom graphs represent susceptible V. vinifera cutlivars. c. Plots of kmer frequencies in six Vitis species. The species phylogeny is shown on the left, with the average detection frequency of R-kmers shown in red dot. The gray dots represent average detection frequencies of randomly chosen kmers that had similar population frequencies in V. arizonica as the set of R kmers. Whiskers denote 95% confidence intervals.

opennotspecifiedJul 2023View details →

FIGURE 4 in Lepanthes cordillerana (Orchidaceae) a new species and the landscape threats to its wild populations

FIGURE 4. Landscape-scale context analysis of Lepanthes cordillerana E.Restrepo, J.S.Moreno & Gal.-Tar. across the three Colombian Andean cordilleras. The boxplots show the median value, the 25th and 75th percentile range for locality (n= 5) across the 10 landscape size (100–2400 m radius). The circular dots represent the outliers in observed records of compositional turnover at each sampled plot. Each boxplot depicts A. Forest cover (percent of forest cover), B. fragmentation (number of patches in a landscape), and C. edge density (total length of forest edge divided by landscape size) context on each population. Prepared by Edicson Parra.

opennotspecifiedJul 2023View details →

FIGURE 3 in Lepanthes cordillerana (Orchidaceae) a new species and the landscape threats to its wild populations

FIGURE 3. Distribution map of Lepanthes cordillerana E.Restrepo, J.S.Moreno & Gal.-Tar. and landscape-scale context of five populations. Green dots represent the recorded populations and digital elevation model from black 0–1000 m to light gray at 3500–5700 m in elevation. Insets show forest cover (dark green) and the matrix (light gray), white buffers depict the 10 landscape sizes where we calculated the habitat loss and configuration metrics. Prepared by Edicson Parra.