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FIGURE 3 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)
FIGURE 3. Ultrametric trees obtained by the two-step method of McCartney & Barreto (2010), showing the divergence times within the family Testudinidae (A) and the divergence times within the C. chilensis complex (B). Numbers above the nodes indicate median of node ages, red numbers below the nodes indicate the clades belonging to the genus Chelonoidis (see table 5).
Figure 6 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 6. Chronogram of Fulgoroidea estimated using the Bayesian phylogenetic by MCMCTREE in paml. Time units are in millions of years. Estimated divergence times are shown near nodes.
Figure 5 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 5. BI analysis (PhyloBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 1 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 1. Sliding window analysis. The red curve shows the value of nucleotide diversity (Pi). Pi value of each PCG is shown below the arrows.
Figure 4 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 4. BI analysis (MrBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 2 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 2. Genetic distance (on average) and ratio of non-synonymous (Ka) to synonymous (Ks) substitution rates.
Figure 3 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 3. ML analysis based on PCG12R–ATP8. Numerals at nodes are bootstrap values (BS). '–' indicates different clades.
Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker
Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.
Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker
Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.
Fig. 8 in Tachypleus syriacus (Woodward)-a sexually dimorphic Cretaceous crown limulid reveals underestimated horseshoe crab divergence times
Fig. 8 Single most parsimonious tree (Tree length 22, Consistency Index 0.909, Retention Index 0.958, Rescaled Consistency Index 0.871) from the dataset in Table S1, also available in the public database Morphobank (Project 1228), analyzed through implicit enumeration with all characters unordered and of equal weight in TNT (Goloboff et al. 2008). Paleolimulus signatus was utilized as the outgroup. Branch support is shown for each node; regular numbers above the node are jackknife values retrieved from 1000 replicates with 33 % deletion, numbers in bold beneath the node are Bremer support values
Fig. 3 in Tachypleus syriacus (Woodward)-a sexually dimorphic Cretaceous crown limulid reveals underestimated horseshoe crab divergence times
Fig. 3 Idealized reconstruction of male and female T. syriacus in amplexus. Drawing by Antony Lamsdell
Fig. 2 T in Tachypleus syriacus (Woodward)-a sexually dimorphic Cretaceous crown limulid reveals underestimated horseshoe crab divergence times
Fig. 2 T. syriacus (Woodward). a MSNM i9352, male. Cretaceous, Lebanon. b MSNM i25083, female. Cretaceous, Lebanon. c MSNM i27468, female. Cretaceous, Lebanon. d MSNM i9351, immature
Fig. 6 T in Tachypleus syriacus (Woodward)-a sexually dimorphic Cretaceous crown limulid reveals underestimated horseshoe crab divergence times
Fig. 6 T. syriacus (Woodward)—BMNH NHM IA 187, soft tissue fluorescence under UV light. a Whole specimen. b Mouth with associated soft-tissue preservation around the prosomal appendage insertions shown in Fig. 5b. c Posterior-most pair of book gills shown in Fig. 5d. d Muscle tissue shown in Fig. 5c. Scale bars: a 50 mm; b, c 10 mm; d 5 mm
Fig. 2 in Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock
Fig. 2 Chronogram of Cichorieae produced by the program BEAST based on ITS1 and ITS2 sequences (unconstrained topology; maximum clade credibility tree with mean node heights obtained by stem group node calibration). Posterior probabilities of nodes are shown
Fig. 3 in Phylogenetic relationships and divergence times of the poorly known genus Spalerosophis (Serpentes: Colubridae)
Fig. 3 Geographical distribution range of the genus Spalerosophis based on data taken from Marx (1959), Baig and Masroor (2008), www.GBIF.org website, and our study
Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone
Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome-wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage-pairs within morphologically defined species, and the lineage-pairs meeting in the contact zones diverged anywhere from 3.1 to 5.8 million years ago. By characterizing patterns of molecular divergence across an average of 11K genes and fitting geographic clines to an average of 7.5K variants, we characterize how patterns of genomic differentiation and introgression change through time. Across this range of divergences, we find that genome-wide differentiation increases but becomes no less heterogeneous. In contrast, we find that introgression heterogeneity decreases dramatically, suggesting that time helps isolated genomes "congeal". Thus, this work emphasizes the pivotal role that history plays in driving lineage divergence.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 3 in Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time
FIGURE 3. Consensus tree from Bayesian phylogenetic analysis. Bayesian posterior probabilities (PP) and ML bootstrap support (BS) are noted at nodes with high support (> 95% PP and 75 BS) and at basal nodes. Nodal support of PP = 1 and BS = 100 are indicated with a solid circle at the branch. Shaded symbols correspond to collection localities on Figure 1.
FIGURE 2. Minimum spanning haplotype networks for all S in Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time
FIGURE 2. Minimum spanning haplotype networks for all S. graciosus group samples sequenced at each of three nuclear loci. Size of each circle corresponds to the frequency of that haplotype. Shading corresponds to clade membership in Figure 3.
FIGURE 1 in Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time
FIGURE 1. Collection localities for samples from the Sceloporus graciosus group included in this study. Colored symbols correspond to clade membership on Figure 3; three individuals for which we only have sequence data at R35 are indicated with stars. Putative species and subspecies boundaries are shaded for the members of the Sceloporus graciosus group. Sceloporus graciosus graciosus: dark gray distribution, S. g. gracilis: light gray distribution, S. g. vandenburgianus: brown distribution, and S. arenicolus: black distribution.
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