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opencc-zeroDec 2018View details →

Data from: Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions, near genes associated with pterin (SPR) and carotenoid metabolism (BCO2), demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been co-opted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles and haplotype analysis revealed abundant trans-specific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

opencc-zeroDec 2016View details →

Data from: Chemical communication, sexual selection, and introgression in wall lizards

Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression, between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters, but the associations were variable and inconsistent between lineages. In experimental contact zones, chemical composition was weakly associated with male reproductive success, and did not predict the likelihood of hybridization. Consistent with these results, introgression of chemical profiles in a natural hybrid zone resembled that of neutral nuclear genetic markers overall, but one compound in particular (tocopherol methyl ether) matched closely the introgression of visual sexual characters. These results imply that associations between male chemical profiles, sexual characters and reproductive success largely reflect transient and environmentally driven effects, and that genetic divergence in chemical composition is largely neutral. We therefore suggest that femoral secretions in wall lizards primarily provide information about residency and individual identity rather than function as sexual signals.

opencc-zeroDec 2014View details →

Data from: Context-dependent expression of sexual dimorphism in island populations of the common wall lizard (Podarcis muralis)

The condition-dependent sexual dimorphism model explains the evolution and maintenance of sexual dimorphism in traits targeted by sexual selection, and predicts that the magnitude of sexual dimorphism depends on the variability of individual condition, male traits being more variable than female corresponding traits. Most convincing examples concern insects, while studies among vertebrates are scanty because manipulating condition often is not possible, and the time to reach sexual maturity may be too long. Islands offer a unique opportunity to compare how the environment affects the expression of sexual dimorphism, since they represent 'natural experimental sets' in which different populations of the same species may experience alternative environmental constraints. We investigated the occurrence of context-dependent expression in sexual dimorphism of head shape in insular populations of the common wall lizards (Podarcis muralis) inhabiting the Tuscan Archipelago (Tyrrhenian Sea). Alternative models were formulated: H0 assumes that the sexual dimorphism is uninfluenced by islands, H1 assumes the only effect of phylogeny, H2A and H2B account for the biogeography of the archipelago (island size and distance from the mainland), while H3 assumes island-specific effects on sexual dimorphism. Models were compared using Akaike's information criterion adjusted for multivariate analyses. All hypotheses performed better than H0, but H3 largely outperformed all other alternative hypotheses, indicating that environmental features of islands play an additive effect to ontogenetic, biogeographic and genetic factors in defining variation in head shape sexual dimorphism. Our results support the hypothesis of a context-dependent sexual dimorphism in common wall lizards

Figure 6 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 6. Observed frequencies for the different character states of the categorical pholidotic characters presenting sufficient variation across the sample examined, and multidimensional scaling (MDS) scatter plot of Manly's overlap index between lineages. White always represents character state 0 and black represents character state 1, except for SL_SUBOC, in which white represents state 4 and black represents state 5. See Table 1 for group codes, Material and methods for variable abbreviations, and Figure 1 for the visual symbols used to represent each lineage.

Figure 5 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 5. Scatter plots of individuals scores (small symbols) and group means (big symbols) of the first three principal components of variation in continuous pholidotic traits for the mitochondrial lineages examined, considering males (top) and females (bottom) separately. The most highly (+, positively; -, negatively) contributing variables (Table 4) are indicated next to each axis. See Table 1 for group codes and Material and methods for variable abbreviations.

Figure 4 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 4. Least-squares means for continuous pholidotic traits in the different mitochondrial lineages examined. Vertical bars denote the observed range. Females of each group are always presented first, denoted with a grey vertical bar, and males are in black. See Table 1 for group codes, Material and methods for variable abbreviations, and Figure 1 for the symbols used to represent each lineage. Notice that no data are available for SCGN and SDLN in the PHJS lineage (Table 3).

Figure 3 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 3. Scatter plots of individual scores (small symbols) and group means (big symbols) of the first three principal components of body shape variation for the mitochondrial lineages examined, considering males (top) and females (bottom) separately. The most highly (+, positively; -, negatively) contributing variables (Table 4) are indicated next to each axis. See Table 1 for group codes and Material and methods for variable abbreviations.

Figure 2 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 2. Least-squares means for multivariate body size and size-corrected biometric variables in the different mitochondrial lineages examined. Only the characters most relevant for global biometric variation and group discrimination (after principle components analysis and canonical variates analysis, respectively; see Results) are presented. Error bars denote ± standard deviation. Females of each group are always presented first, denoted with a grey vertical bar, and males are in black. See Table 1 for group codes, Material and methods for variable abbreviations, and Figure 1 for symbols used to represent each lineage.

Figure 1 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 1. Mitochondrial DNA lineages sampled, maximum likelihood tree of phylogenetic relationships between them (A, modified from Kaliontzopoulou et al., 2011), and map of the localities from which the samples analysed morphologically were obtained (B).

Figure 3 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 3. Example of Grad-CAM heatmaps obtained for Podarcis lusitanicus. The upper images show two common patterns observed in male dorsal images (also found, albeit with some differences, in females). The bottom images exhibit the patterns most frequently found in male and female head lateral images (here illustrated in two females).

Figure 2 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 2. Confusion matrix for male (upper) and female (lower) image classification for the two-class case based on a combination of predictions from six models. Abbreviations used: Pboc, P. bocagei; Plus, P. lusitanicus.

Highly variable (no clear pattern). All portions of the dorsal views were equally used. In head images the area around the eye, the top of the head, the snout and the throat were all used in similar proportions. P. carbonelli Variable for both views. Snout and middle of the dorsum used in dorsal view. Top of the head most frequently (but not strictly) used in lateral view. P. guadarramae Whole body used for dorsal view (but variable); either throat (most common) or ear region used in head lateral views. P. hispanicus Variable. Anterior portion of snout used more frequently than in other species for both dorsal and head lateral views. P. liolepis Highly variable. Whole body used in most dorsal images, area around the eye and throat used in head lateral views, but other patterns common. P. lusitanicus Highly variable. All parts of the dorsum used (but frequently the most posterior part); area around the ear frequently used in head lateral images. P. tunesiacus Highly variable. Dorsal area near the insertion of the posterior limbs used more frequently than in other species; different regions of the head used, often simultaneously. P. Ʋaucheri Highly variable. Different regions of dorsum (from head to the posterior region) used in dorsal images, all portions of the head, but most frequently the throat, used in lateral images. P. Ʋirescens Highly variable. All parts of both images used. Head and anterior part of the dorsum more used than in other species. in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Highly variable (no clear pattern). All portions of the dorsal views were equally used. In head images the area around the eye, the top of the head, the snout and the throat were all used in similar proportions. P. carbonelli Variable for both views. Snout and middle of the dorsum used in dorsal view. Top of the head most frequently (but not strictly) used in lateral view. P. guadarramae Whole body used for dorsal view (but variable); either throat (most common) or ear region used in head lateral views. P. hispanicus Variable. Anterior portion of snout used more frequently than in other species for both dorsal and head lateral views. P. liolepis Highly variable. Whole body used in most dorsal images, area around the eye and throat used in head lateral views, but other patterns common. P. lusitanicus Highly variable. All parts of the dorsum used (but frequently the most posterior part); area around the ear frequently used in head lateral images. P. tunesiacus Highly variable. Dorsal area near the insertion of the posterior limbs used more frequently than in other species; different regions of the head used, often simultaneously. P. Ʋaucheri Highly variable. Different regions of dorsum (from head to the posterior region) used in dorsal images, all portions of the head, but most frequently the throat, used in lateral images. P. Ʋirescens Highly variable. All parts of both images used. Head and anterior part of the dorsum more used than in other species.

Figure 1 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 1. The two image types analysed in this study (before pre-processing): above, a dorsal view; below, a head lateral image. Both images correspond to the same Podarcis Ʋaucheri s.l. male.

Highly variable. Mid-portion of the dorsum used frequently (although other areas as well). Tip of the snout used often, but area around the ear and throat are also relevant. P. carbonelli Variable. In the dorsal view, the tip of the snout is frequently used. In the head lateral view, the tip of the snout is also com- monly used, as well as the most posterior region of the head. P. guadarramae Variable. Mid portion of the dorsum and tip of the snout are the regions used more frequently in dorsal and head lateral views, respectively. P. hispanicus Variable. The head and most anterior part of the dorsum are frequently used in the dorsal view. Snout and/or top of posterior region of head used. P. liolepis Variable. Different parts of the dorsum are used, whereas the tip of the snout is used in most head lateral images. P. lusitanicus Anterior dorsum, in the dorsal view, and both snout and posterior side of the head (in head lateral views) frequently used. P. tunesiacus Variable. Tip of the snout and posterior part of the trunk more used than in other species; snout and top head region behind the eye used with some frequency. P. Ʋaucheri Highly variable. All parts of the dorsum used in dorsal images, various parts of the head (but frequently snout and throat combined) used in head lateral images. P. Ʋirescens Highly variable. All portions of the dorsum used in dorsal images, region around and behind the ear more used than in other species for head lateral images. in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Highly variable. Mid-portion of the dorsum used frequently (although other areas as well). Tip of the snout used often, but area around the ear and throat are also relevant. P. carbonelli Variable. In the dorsal view, the tip of the snout is frequently used. In the head lateral view, the tip of the snout is also com- monly used, as well as the most posterior region of the head. P. guadarramae Variable. Mid portion of the dorsum and tip of the snout are the regions used more frequently in dorsal and head lateral views, respectively. P. hispanicus Variable. The head and most anterior part of the dorsum are frequently used in the dorsal view. Snout and/or top of posterior region of head used. P. liolepis Variable. Different parts of the dorsum are used, whereas the tip of the snout is used in most head lateral images. P. lusitanicus Anterior dorsum, in the dorsal view, and both snout and posterior side of the head (in head lateral views) frequently used. P. tunesiacus Variable. Tip of the snout and posterior part of the trunk more used than in other species; snout and top head region behind the eye used with some frequency. P. Ʋaucheri Highly variable. All parts of the dorsum used in dorsal images, various parts of the head (but frequently snout and throat combined) used in head lateral images. P. Ʋirescens Highly variable. All portions of the dorsum used in dorsal images, region around and behind the ear more used than in other species for head lateral images.

Figure 4 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 4. Confusion matrix for male (upper) and female (lower) image classification for the nine-class experiment based on a combination of predictions from six models. Abbreviations used: Pboc, P. bocagei; Pcar, P. carbonelli; Phis, P. hispanicus; Plio, P. liolepis; Plus, P. lusitanicus; Pvsl, P. Ʋaucheri s.l.; Pvss, P. Ʋaucheri s.s.; Pvir, P. Ʋirescens.