Fig 1.
Geographic location of the fossil sites considered in the study.
Northeastern Mexico: C = Cedral, J = San Josecito Cave; American Southwest: A = Algerita Blossom Cave, M = Big Manhole Cave, L = Blackwater Draw, K = Dark Canyon Cave, D = Dry Cave, X = El Barreal, F = Fresnal Canyon, G = Highway 45, Chihuahua, I = Isleta Cave No. 2, O = Lubbock Lake, H = Nash Draw, Q = Quitaque Creek, S = Salt Creek, R = Scharbauer Ranch, U = U-Bar Cave, V = Villa Ahumada; Wyoming: N = Natural Trap Cave; Alberta: E = Edmonton area gravel pits, W = Wally’s Beach site; Yukon Territory: B = Bluefish Caves.
Fig 2.
Upper (A) and lower (B) fourth premolars showing the dental structures referred to in the text, following the dental nomenclature of Evander [64]. Computed tomography (CT-scan) images of LACM 192/156497 (A) and TMM 937–169 (B). The anterior side of both teeth is located to the right. The lingual side is located at the bottom in figure A and the top in figure B.
Fig 3.
Lower (A and B) and upper (C and D) third premolars showing the measurements collected for lower and upper cheek teeth. Transverse width (Tr) and anteroposterior length (Ap) measurements are shown in figures A and C. These measurements were taken at a tooth crown height of 2 cm. In the lower teeth the measurements were taken 2 cm above from the bifurcation of the protoconid and hypoconid columns measured on the buccal side of the tooth (B). In the upper teeth the measurements were taken 2 cm above from where the mesostyle ends on the buccal side of the tooth (D). Figures A and B: left p3 (DhPg-8 3437.1). Figures C and D: right P3 (DP 3850).
Fig 4.
Occlusal surface of a P3 (LACM 192/18109) showing the 24 landmarks used in the analysis.
Refer to the main text and Table C in S2 File for a description of the landmarks and details about how they were digitized.
Fig 5.
Digitized double knot (metaconid, linguaflexid, and metastylid) of a lower p4 (KU 50629) showing the 50 landmarks used in the analysis.
Refer to the main text for details about how the landmarks were digitized.
Fig 6.
Principal component plots and histograms of PC 1 scores resulting from PCA of the linear measurements of upper M1/M2 teeth.
The specimens come from five geographic regions of the Western Interior of North America: Mexico (C, Cedral; J, San Josecito Cave), the American Southwest (A, Algerita Blossom Cave; D, Dry Cave; F, Fresnal Canyon; K, Dark Canyon Cave; H, Nash Draw; I, Isleta Cave No. 2; L, Blackwater Draw; M, Big Manhole Cave; P, Imperial; R, Scharbauer Ranch; S, Salt Creek; U, U-Bar Cave); Wyoming (N, Natural Trap Cave); Alberta (E, Edmonton area gravel pits; W, Wally’s Beach), and the Yukon Territory (B, Bluefish Caves). A lower case “a” beside the specimen symbol indicates a tooth that yielded ancient mtDNA (EQ16 from Dry Cave). An asterisk (*) beside the specimen symbol denotes a tooth associated (i.e., it belongs to the same individual) with a specimen from which ancient mtDNA was obtained (teeth associated with EQ3 from Dry Cave, EQ9 from Natural Trap Cave, EQ29 and EQ43 from Wally’s Beach, EQ44 and EQ47 from Bluefish Caves). The dark line in the histograms corresponds to the kernel density estimation. Table C in S1 File lists all of the specimens included in this analysis.
Table 1.
Eigenvalues, percentage variance, and factor loadings for the principal components resulting from PCA of the linear measurements of the upper teeth (Ap = anteroposterior length; Tr = transverse width), taken at a crown height of 2 cm.
Table 2.
Eigenvalues, percentage variance, and factor loadings for the principal components resulting from PCA of the linear measurements of the lower teeth (Ap = anteroposterior length; Tr = transverse width), taken at a crown height of 2 cm.
Table 3.
Results of Shapiro-Wilk test for normal distribution of principal component 1 scores for each tooth category and geographic region studied.
Fig 7.
Plot of the first two Canonical Variates resulting from CVA of 24 landmark coordinates of the occlusal enamel pattern of the upper premolars (P3/P4).
Shown on the margins of the graph is the change in tooth shape along each corresponding axis. The groups included in the analysis are: 1) large specimens from Cedral, Mexico (Cl); 2) medium specimens from Cedral (Cm) as well as all teeth from San Josecito Cave (J), Mexico; 3) small specimens from Cedral, Mexico (Cs); 4) large specimens from different localities of the American Southwest (identified by a lower case “l” beside the specimen symbol; refer to Fig 1 for locality names); 5) medium specimens from different localities of the American Southwest (identified by a lower case “m” beside the specimen symbol; refer to Fig 1 for locality names); 6) medium specimens from Natural Trap Cave, Wyoming (N); 7) large specimens from Natural Trap Cave, Wyoming (Nl); 8) large specimens from the Edmonton area gravel pits (E) and Wally’s Beach (W), Alberta; and 9) all of the specimens digitized from Bluefish Caves, Yukon (B). A lower case “a” beside the specimen symbol indicates a tooth that yielded aDNA (these include EQ38 and EQ45 from Bluefish Caves). An asterisk (*) beside the specimen symbol denotes a tooth associated (i.e., it belongs to the same individual) with a specimen from which aDNA was obtained (including teeth associated with EQ3 from Dry Cave, New Mexico, EQ9 from Natural Trap Cave, EQ43 from Wally’s Beach, and EQ44 as well as EQ47 from Bluefish Caves). Table A in S2 File lists all of the specimens included in this analysis.
Fig 8.
Plot of the first and third Canonical Variates resulting from CVA of 24 landmark coordinates of the occlusal enamel pattern of the upper premolars (P3/P4).
Shown on the margins of the graph is the change in tooth shape along each corresponding axis. Refer to caption of Fig 7 for details on the specimens included in this analysis.
Table 4.
Eigenvalues, percentage variance, and cumulative percentage variance of the first five Canonical Variates resulting from CVA of 24 landmark coordinates of the occlusal enamel pattern of the upper premolars (P3/P4).
Table 5.
Procrustes distances among groups for the upper premolars (P3/P4).
Table 6.
P-values from permutation tests (10,000 permutation rounds) for Procrustes distances among groups of the upper premolars (P3/P4).
Fig 9.
Plot of the first two Canonical Variates resulting from CVA of 50 landmark coordinates of the double knot (metaconid-linguaflexid-metastylid complex) of the lower premolars (p3/p4).
Shown on the margins of the graph is the change in shape along each corresponding axis. The groups included in the analysis are: 1) large specimens from Cedral, Mexico (Cl); 2) medium specimens from Cedral (Cm) as well as all teeth from San Josecito Cave (J), Mexico; 3) small specimens from Cedral, Mexico (Cs); 4) large specimens from different localities of the American Southwest (identified by a lower case “l” beside the specimen symbol; refer to Fig 1 for locality names); 5) medium specimens from different localities of the American Southwest (identified by a lower case “m” beside the specimen symbol; refer to Fig 1 for locality names); 6) small specimens from Villa Ahumada (Vs) and Highway 45 (Gs), Chihuahua, Mexico; 7) medium specimens from Natural Trap Cave, Wyoming (N); 8) large specimens from Natural Trap Cave, Wyoming (Nl); 9) large specimens from the Edmonton area gravel pits (E) and Wally’s Beach (W), Alberta; 10) medium specimens from the Edmonton area gravel pits (Em), Alberta; and 11) all of the specimens digitized from Bluefish Caves, Yukon (B). A lower case “a” beside the specimen symbol indicates a tooth that yielded aDNA (these include EQ1 from Dry Cave, New Mexico, EQ4 from the Edmonton area gravel pits, EQ13 as well as EQ22 from Natural Trap Cave, EQ43 from Wally’s Beach, and EQ39, EQ48, and EQ50 from Bluefish Caves). An asterisk (*) beside the specimen symbol denotes a tooth associated (i.e., it belongs to the same individual) with a specimen from which aDNA was obtained (including teeth associated with EQ42, EQ51, and EQ53 from Bluefish Caves). Table B in S2 File lists all of the specimens included in this analysis.
Fig 10.
Plot of the first and third Canonical Variates resulting from CVA of 50 landmark coordinates of the double knot (metaconid-linguaflexid-metastylid complex) of the lower premolars (p3/p4).
Shown on the margins of the graph is the change in shape along each corresponding axis. Refer to caption of Fig 9 for details on the specimens included in this analysis.
Table 7.
Eigenvalues, percentage variance, and cumulative percentage variance of the first five Canonical Variates resulting from CVA of 50 landmark coordinates of the double knot (metaconid-linguaflexid-metastylid complex) of the lower premolars (p3/p4).
Table 8.
Procrustes distances among groups for the lower premolars (p3/p4).
Table 9.
P-values from permutation tests (10,000 permutation rounds) for Procrustes distances among groups of the lower premolars (p3/p4).
Fig 11.
Consensus tree of Bayesian (Markov chain Monte Carlo) phylogenetic analysis displaying relationships between mitochondrial control region (HVR 1) haplotypes of extinct and extant equids, rooted with domestic donkey (Equus africanus asinus (L., 1758)) and Somali Wild Ass (Equus africanus somaliensis (Noack, 1884)) as the outgroup.
The tree was constructed using 588 bp fragments of the HVR I. Posterior probabilities of the major nodes are listed for each of the branches. The groups discussed in the text are indicated by the letters. Tables D and F in S2 File list all of the specimens included in this analysis.
Table 10.
Summary of the results of the geometric morphometric analyses of the cheek teeth and the Bayesian phylogenetic analysis of ancient mtDNA.