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FIGURE 6 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 6. Species tree produced by SVDQuartets. The species tree branch lengths are equal and bootstrap support was maximal for all nodes and not shown. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated with McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) in bold text. For Rainbow Trout subspecies, sampling locations are labeled with a four-letter code corresponding to Figure 1 and Table 1. The two samples of Lahontan Cutthroat Trout (O. clarkii henshawi) are labeled as LCT.

FIGURE 2 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 2. Principal Component Analyses. The first two Principal Components (PCs) are presented for all samples (n = 318) in the population genetics analysis in A and Redband Trout samples (n = 204) in B. Genotype likelihoods were generated separately for the PCs presented in each panel. In A points are color coded by Group corresponding broadly to lineage, and further condensed into a Major Group by consolidating the California Golden Trout Complex and represented by shape (Table 1). In B, points are colored by watershed and the same shape applied to the Major Group (MRRB and REDB). Abbreviations for Major Group are explained in the text.

FIGURE 1 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 1. Map of key features and distributions of key lineages in this study. The distribution of Coastal Rainbow Trout (Oncorhynchus mykiss irideus) is shown in grey shading. Other lineages are labeled in different colors. Distributions were retrieved from the PISCES database (pisces.ucdavis.edu, "Historic Range—Expert Opinion") except for Warner Lakes Redband Trout (O. m. ssp.), which is represented by a polygon of hydrologic unit code (HUC) 17120007. Sampling locations used in phylogenetic analyses are indicated with a four-letter code that corresponds to Table 1 and Supplemental Table S1. Samples of O. m. gairdnerii from Idaho are not shown.

FIGURE 5 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 5. Maximum Likelihood (ML) tree (A) and ML consensus tree (B). In both panels subspecies of Rainbow Trout (Oncorhynchus mykiss) are indicated along with members of the Golden Trout Complex. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) are indicated with bold text. Individual sample names are provided at tips and further described in Table 1. In 5A, nodes receiving Shimodaira-Hasegawa approximate Likelihood Ratio Test scores> 80 and bootstrap support (BS)> 95% are indicated with a diamond. In 5B, two spans of bootstrap support are presented, with 100%> BS> 95% as solid black circles and 95%> BS> 90% as grey circles at nodes.

FIGURE 8 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 8. McCloud River Redband Trout, Onchorhynchus mykiss calisulat, ssp. nov., Sheepheaven Creek. A. WFB 5020, holotype, 120 mm SL. B. same specimen as in A, radiograph. C. TCWC 28772.01, paratype, 144 mm SL. D. Illustration of O. m. calisulat, ssp. nov., showing life colors, © J. Tomelleri, used with permission.

FIGURE 4 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 4. Admixture plots from McCloud river trout and other Redband Trout in population genetics dataset. Admixture results from NGSAdmix for genetic clusters (K) from 2-4 with the subset of samples collected as Redband Trout. Sample size of 204, optimal K = 2. The x-axis labels are labeled according to watershed.

Fig. 6 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

Fig. 6.—Landscape connectivity analysis based on the Intron 7 of the beta fibrinogen shared haplotypes in Reithrodontomys microdon. A) Ecological niche modelling of R. microdon; warmer colors depict high suitability areas. B) Friction layer obtained from the Ecological niche modelling; warmer colors depict areas with a high cost to dispersal. C) Fgb haplotype network and dispersal network with the least-cost paths; warmer colors depict paths traversed more frequently and higher population connectivity. The black circles and triangle represent the occurrence points of R. microdon and R. bakeri, respectively.

Fig. 4 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

Fig. 4.—Phylogenetic relationships among species of the Reithrodontomys tenuirostris group using a concatenated sequences data set (Cytochrome b + Intron 7 of the beta fibrinogen). Values below branches represent nodal support for BI analysis. Terminal labels are named according to mammal collection voucher numbers (see Supplementary Appendix I).

Fig. 1 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

Fig. 1.—Map of Mexico and Central America showing localities for specimens of the Reithrodontomys tenuirostris species group analyzed in this study. Dotted dots represent the geographical distribution (proposed by Hall 1981) of the R. microdon subspecies [a) R. m. wagneri; b) R. m. albilabris; c) R. m. microdon]. Gray hues depict an elevation gradient: white <800 m; light gray 800–1700 m; and dark gray>1700 m.

Fig. 3 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

Fig. 3.—Phylogenetic relationships among species of the Reithrodontomys tenuirostris group using sequences data of the Intron 7 of the nuclear gene beta fibrinogen. Values below branches represent nodal support for BI/ML analysis. Terminal labels are named according to mammal collection voucher numbers (see Supplementary Appendix I).

Fig. 5.—Maximum clade credibility tree obtained with BEAST2 in Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

Fig. 5.—Maximum clade credibility tree obtained with BEAST2 for species of the Reithrodontomys tenuirostris group using Cytochrome b sequences data. Values above branches represent mean divergence times and below the 95% highest posterior density (HPD) intervals. Dark gray bars represent taxa delimited as species-level by the single-locus methods mPTP and bGMYC with probability values above 0.95, and the multiple-loci method STACEY.

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FIG. 2 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 2. Strict consensus tree of the 30,000 most parsimonious trees based on the combined trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 1 (not weighted) including 58 taxa; Length = 524, CI = 0.479, RI = 0.601, RC = 0.288. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.

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FIG. 1 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 1. Strict consensus tree of the 30,000 most parsimonious trees based on the 5S spacer sequence data recoverd during heuristic Search 3 for 56 taxa; Length = 231, CI = 0.519, RI = 0.743, RC = 0.386. Values above the internodes give the jackknife values (where absent, the jackknife values are less than 50%). Members of the Lampranthus group are underlined.

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FIG. 3 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data

FIG. 3. Strict consensus tree of the 167 most parsimonious trees based on the combined and successively weighted trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 4 including 51 taxa; CI = 0.599, RI = 0.841, RC = 0.504. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.

FIGURE 2 in Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

FIGURE 2. Bayesian phylogenetic tree of Jania species (Rhodophyta) based on cox1 gene with focus on specimens from south-eastern Australia. Numbers above branches represent posterior probabilities (values <0.5 were omitted). Some branches were shortened to fit the figure. Specimens sequenced in this study marked in bold and have their herbarium code identified. Colored columns indicate species delimitation methods results: ABGD; ASAP P (p-value partition), ASAP W (w rank partition); GMYC S (single-threshold), GMYC M (multiple-threshold); PTP B (Bayesian inference), PTP M (Heuristic or Maximum Likelihood); and SPN 95% and 99% of parsimony probability limit. Black column indicates the consensus across all species delimitation results. Numbers below to each column indicate the total number of species partitions for each method or the consensus. Jania squamata in the PTP B result was divided into three different species.

FIGURE 3 in Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

FIGURE 3. Maximum likelihood phylogeny of Jania species based on psbA gene focusing on specimens from south-eastern Australia. Numbers above branches represent non-parametric bootstrap support (values <70 omitted). Species names are followed by GenBank accession number and specimen locality (for sequences downloaded from GenBank), or species name, herbarium codes for all specimens sharing that particular haplotype, and specimen locality (marked in bold for sequences produced in this study). Scale bar = substitutions per site.

FIGURE 1 in Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

FIGURE 1. Maximum likelihood phylogenetic tree of Jania species (Rhodophyta) based on cox1 gene with focus on specimens from south-eastern Australia. Numbers above branches represent non-parametric bootstrap support (values <70 omitted). Tree tip names are composed by species name, GenBank accession number and specimen locality (for sequences downloaded from GenBank), or species name, herbarium code for all sequenced specimens presented by that sequence, and specimen locality (for sequences produced in this study, all marked in bold). Scale bar = substitutions per site.

FIGURE 4 in Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

FIGURE 4. Bayesian phylogenetic tree of Jania species based on psbA gene with focus on specimens from south-eastern Australia. Numbers above branches represent posterior probabilities (values <0.5 omitted). Specimens sequenced in this study are marked in bold and have their herbarium code identified. Colored columns indicate species delimitation results: ABGD; ASAP P (p-value partition), ASAP W (w rank partition); GMYC S (single-threshold), GMYC M (multiple-threshold); PTP B (Bayesian inference), PTP M (Heuristic or Maximum Likelihood); and SPN 95% and 99% of parsimony probability limit. Black column indicates the consensus across all species delimitation results. Numbers below each column indicate the total number of species partitions for each method, including the consensus.

FIGURE 5 in Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

FIGURE 5. Maximum likelihood phylogenetic tree of Corallina species based on psbA DNA sequences. Numbers above branches represent non-parametric bootstrap support. Values <50 were omitted. Species names are followed by GenBank accession number. South-eastern Australian sequences produced in this study are marked in bold. Bossiella, Calliarthron and Arthrocardia were used as outgroups.