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22 results for “Liolaemus darwinii”
Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consist of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy decreased when using only one individual per species or 25% of the full sequence length. In addition, locus 'informativeness' was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed towards further assessment of other factors that can impact performance of species trees, including gene flow, data 'informativeness', tree shape, missing data, and uncertain species boundaries.
FIGURE 2 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Catamarca Province, Argentina
FIGURE 2. Distribution of Liolaemus crepuscularis (white circles) and members of the ornatus group, plus L. espinozai. The arrow indicates the type locality.
FIGURE 3 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Catamarca Province, Argentina
FIGURE 3. Phylogeny of the darwinii group fom total evidence (morphology and molecular) analysis. (From Abdala, 2005). The arrow indicates Liolaemus crepuscularis.
FIGURE 2 in A new Andean species of Liolaemus of the darwinii Complex (Reptilia: Iguanidae)
FIGURE 2. View looking toward the south at the habitat of Liolaemus montanezi. In the foreground, sparse bushes of Monte vegetation. Behind, the high slope that limits to south the Parque Nacional San Guillermo. The slopes of Sierra de los Médanos are seen in the far background.
FIGURE 6 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 6. Cladogram of the L. darwinii group, proposed for Abdala (2007), based on total evidence analysis of the L. boulengeri group.
FIGURE 5 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 5. Map showing the distribution of L. diaguita and the species of the L. darwinii group more close distributed. Black square: L. diaguita. Black circle: L. quilmes. Black triangle: L. espinozai. Black star: L. koslowskyi. Black diamond: L. abaucan. White square: L. albiceps. White circle: L. lavillai. White triangle: L. calchaqui. White star: L. crepuscularis. Arrow indicates the type locality of L. diaguita.
FIGURE 1 in A new species of Liolaemus from the darwinii group (Iguania: Liolaemidae), Tucumán province, Argentina
FIGURE 1. Localities for three populations of L. quilmes (triangles) compared to the new species (star), from North to South: L. quilmes (Holotype): 3.2 km south of Animaná, Ruta Nacional 40, Cafayate Department, Salta Province (25º59´S, 65º58´W, 1695 m); Ruinas de Quilmes, Tafí del Valle Department, Tucumán Province (26º28´15" S, 66º02´05" W, 1978 m); El Tio, Tafí del Valle Department, Tucumán Province (26º35.4´S, 65º52.8´W, 2148m); Liolaemus pacha sp. nov. (Holotype), Km 98, Ruta Provincial 307 (Los Cardones), Tafí del Valle Department, Tucumán Province (26º40´1.5" S, 65º49´5.1" W, 2725 m).
FIGURE 10 in A new species of Liolaemus from the darwinii group (Iguania: Liolaemidae), Tucumán province, Argentina
FIGURE 10. Lorilabials and supralabials alternating between light and dark color. Top: infralabials with diffuse spots in Liolaemus pacha sp. nov.; bottom: infralabials with marked spots in L. quilmes (drawing VJH).
Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)
Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate non-monophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian Computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.
Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)
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Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)
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Data from: Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling
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FIGURE 1a in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Catamarca Province, Argentina
FIGURE 1a. Liolaemus crepuscularis (holotype, FML 16622). Male, 56.7 mm SVL.
FIGURE1b in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Catamarca Province, Argentina
FIGURE1b. Liolaemus ornatus. Adult male, from Abrampampa, Jujuy Province, Argentina
FIGURE 1 in A new Andean species of Liolaemus of the darwinii Complex (Reptilia: Iguanidae)
FIGURE 1. The holotype of Liolaemus montanezi, adult male, in life.
FIGURE 1 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 1. Adult male of L. diaguita sp nov., dorsal view.
FIGURE 3 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 3. Adult female of L. diaguita sp nov., dorsal view
FIGURE 2 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 2. Adult male of L. diaguita sp nov., ventral view.
FIGURE 4 in A new species of the Liolaemus darwinii group (Iguania: Liolaemidae) from Salta Province, Argentina
FIGURE 4. Adult female of L. diaguita sp nov., ventral view.
FIGURE 5 in A new species of Liolaemus from the darwinii group (Iguania: Liolaemidae), Tucumán province, Argentina
FIGURE 5. Marking patterns in Liolaemus pacha sp. nov. Left: dorsal; right: ventral (drawing VJH).
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