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Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this dataset, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this dataset. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled datasets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps.
FIGURE 5 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 5. Color pattern variation in B. bramei. A. Specimen from the type locality; note the rust colored patches over the shoulders. The presence of these patches is typical of B. bramei. B. MVZ 267142, from Tobias Creek, Tulare Co., California. C–F. Four specimens from Cannell Creek, Kern and Tulare counties, California, showing range of coloration found in this population. The bold red coloring is not known from other populations. Refer to the web version of this article for color figure.
FIGURE 6 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 6. Habitats occupied by B. bramei in the Kern River Canyon. A. Type locality, Packsaddle Canyon, 1135 m elev., Tulare Co., California (photo taken 5 March 2011). On the east side of the Kern River, salamanders are often associated with metamorphic rock in seepage areas as shown here. B–D. On the west side of the Kern River, B. bramei has been found in a diversity of habitats including the following: B. under isolated cover objects in oak grassland S of Kernville, Kern Co., California (photo taken 21 March 2008); C. in pine litter along Tobias Creek, Tulare Co., California (photo taken 22 March 2007) and D. under rocks and in leaf litter N of South Falls Creek, Tulare Co., California (photo taken 28 January 2010; numerous individuals were found on this date). Refer to the web version of this article for color figure.
FIGURE 4 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 4. Holotype of B. bramei (MVZ 217944). A. Digital x-ray of skull and forelimbs. Digital x-rays were processed using the levels and curves functions in Adobe Photoshop. B. Photo of holotype in life.
FIGURE 2 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 2. Overview of relationships in the subgenus Batrachoseps, based on cob dataset analyzed by Jockusch and Wake (2002). The four major clades are named (attenuatus, Sierran, pacificus and nigriventris groups) and terminals are labeled in all groups except the nigriventris group. Shaded boxes indicate the four geographic units of B. relictus, as recognized by Brame and Murray (1968). Terminal taxa that do not contain populations previously placed in B. relictus are collapsed. Note that topotypic B. relictus are not included in this tree. The clade labeled 'Greenhorns' has been retained in B. relictus until the present, but is described here as B. altasierrae sp. nov.
FIGURE 8. Allozyme analyses. A in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 8. Allozyme analyses. A. Minimum evolution tree showing the relationships of 14 populations based on Nei's (1978) D (Table 4) for 27 variable loci included in allozyme study 1. The topology of the neighbor-joining tree is identical. B. Multidimensional scaling of Nei's (1978) D (Table 5) for eight populations from the nigriventris group based on allozyme study 2. Note the intermediate position of the Cannell Creek (CAN) population between B. bramei from Fairview (FAI) and B. simatus from Erskine Creek (ERS). See Table 5 for abbreviations. Sampling localities are listed in Table 3.
FIGURE 1. A in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 1. A. Map of California, USA, showing the ranges of Batrachoseps nigriventris group species and other species of Batrachoseps from the vicinity of the Kern River Canyon. The range of B. relictus in the Lower Kern River Canyon is contained within the range of B. simatus. Individual dots indicate isolated populations of B. altasierrae sp. nov. from the Kern Plateau (blue) and of B. robustus from the Scodie Mountains (green). B. Point localities for Batrachoseps from the Kern River Canyon and vicinity. Localities include all identified specimens from the collection of the Museum of Vertebrate Zoology, University of California, Berkeley, as well as additional specimens from the California Academy of Sciences and, for B. relictus, from the Los Angeles County (California) Museum. Lighter shading indicates higher elevation; blue indicates major streams or rivers. Type localities are indicated by open symbols for all species except B. gregarius (whose type locality is outside of the region shown). Refer to the web version of this article for color figure.
FIGURE 7. B. altasierrae and B. relictus. A in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 7. B. altasierrae and B. relictus. A. Holotype of B. altasierrae. B. B. altasierrae from the type locality in life (no voucher). C. Digital x-ray of the skull and forelimbs of an adult female B. altasierrae (MVZ 156394, SL = 39.9 mm) from Sugarloaf Peak, Tulare Co., California. D. Adult B. relictus from Breckenridge Mountain, Kern Co., California in life (no voucher). E. Digital x-ray of the skull and forelimbs of an adult (SL = 45.3 mm) female B. relictus from Breckenridge Mountain (MVZ 267114). F. Type locality of B. altasierrae. G. High elevation site on Breckenridge Mountain, Kern Co., California at which specimens referred here to B. relictus were discovered. Nearly all individuals at this locality have been found within the seep shown in the foreground. Habitat photos taken on 28 May 2011. Refer to the web version of this article for color figure.
FIGURE 3 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 3. Morphological comparisons of Batrachoseps from the Kern River Canyon. A–F. Principal components analysis of correlation matrix of regression residuals of specimens from in and around the Kern River Canyon. Each color/symbol combination indicates a population. A–C compare B. relictus from the Lower Kern River Canyon, two candidates for inclusion in B. relictus (Breckenridge Mountain represented by the Lucas Creek and Squirrel Meadow populations and Greenhorn Mountains 1 and 2 from north of the Kern River), and B. kawia, which is the sister taxon to the Greenhorn populations. D–F show differentiation of the Upper Kern River Canyon populations (magenta), described here as Batrachoseps bramei sp. nov., from their close relatives B. gregarius (gray) and B. simatus (black). G–J. Boxplots of principal components (G–I) and SL (J) for species in and around Kern River Canyon. Refer to the web version of this article for color figure.
FIGURE 9 in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 9. Samples included in the cob phylogeny of the Batrachoseps nigriventris group. A. Map of California, showing topographic relief, with localities for specimens from outside of the Kern River Canyon (black symbols). Box shows approximate area of panel B. B. Kern River Canyon, showing localities for specimens from the Kern River Canyon and Breckenridge Mountain. Major side drainages are labeled. For clarity, streams on the north side of the Lower Kern River Canyon are omitted.
FIG. 7 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 7. Distribution of B. wakei. (A) Topographic relief map, with black dots marking the four localities at which B. wakei has been found; population numbers are as in Table 1. White dots indicate nearby localities for B. nigriventris on Vandenberg Space Force Base. Map tiles by Stamen Design, under a CC BY 3.0 license. Map data by OpenStreetMap under ODbL. (B) Inset of coastal region showing hypothesized range of B. wakei.
FIG. 9 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 9. Haplotype networks and geographic variation in allele frequencies for the two loci showing variability in B. wakei. Haplotype networks for rag1 (A) and gapdh (B), with circle size scaled to allele frequency and shading indicating the four source populations. Distribution of alleles across geography for rag1 (C) and gapdh (D), with circle size scaled to sample size from the population, and shading distinguishing the three alleles.
FIG. 6 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 6. Dorsal view of the right front and hind foot of an adult male Batrachoseps wakei (CCBER 32847, SVL ¼ 55.8 mm); cartilage is stippled. Scale bar ¼ 2 mm.
FIG. 8 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 8. Habitat of B. wakei. (A) Type locality at Point Arguello, California, USA; (B) northernmost locality at Honda Point, California, USA. Photographs Ivan Parr, used with permission.
FIG. 5 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 5. Skull of an adult female Batrachoseps wakei (CCBER 32848, SVL ¼ 53.0 mm); anterior ventral (top) and dorsal (bottom) views; bones, teeth, and cartilage (stippled) are shown. Scale bar ¼ 2 mm.
FIG. 4 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 4. Comparisons of body proportions in B. wakei and its closest relatives. (A) Head length (snout to gular fold); (B) maximum head width; (C) hind limb length; and (D) tail length versus snout–vent length (SVL); color and shape indicate species.
FIG. 2 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 2. Photos of Batrachoseps wakei. (A) Paratype (MVZ 293139, adult male, SVL ¼ 60.4 mm) in life; (B) paratype of B. wakei (MVZ 293140, adult male, SVL ¼ 63.0 mm) contrasted with B. nigriventris from Honda Canyon, Santa Barbara Co., California, in close parapatry with B. wakei; (C) EL J 1662. Photos A, B by Sam Sweet; photo C Iñigo Martínez-Solano, used with permission.
FIG. 3 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 3. Head shape in ventral view of (A) Batrachoseps wakei (CCBER 32844, adult female, SVL ¼ 67.6 mm); (B) Batrachoseps major (SSS 34390, adult female, SVL ¼ 66.5 mm); and (C) Batrachoseps pacificus (SBMNH 654, adult female, SVL ¼ 67.0 mm); scale bar ¼ 5 mm.
FIG. 1 in A New Relict Species of Slender Salamander (Plethodontidae: Batrachoseps) with a Tiny Range from Point Arguello, California
FIG. 1. Distribution and relationships of the B. pacificus group. (A) Colored polygons show the ranges of the seven species currently recognized in B. pacificus (based on IUCN range polygons), and black dots show the locations of molecular samples included in this study; brown polygon shows range of B. nigriventris. Arrow and purple circle indicate the locality of the species described here. Map tiles by Stamen Design, under a CC BY 3.0 license. Map data by OpenStreetMap under ODbL. (B) Species tree for the B. pacificus group and selected outgroups inferred from coalescent analysis of seven nuclear and one mitochondrial marker. Support values are ASTRAL-III's local posterior probabilities; branch lengths are in coalescent units. See Data Accessibility for tree file.
Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
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