Research Article |
Corresponding author: Jackie L. Childers ( jchilders@berkeley.edu ) Academic editor: Johannes Penner
© 2021 Jackie L. Childers, Sebastian Kirchhof, Aaron M. Bauer.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Childers JL, Kirchhof S, Bauer AM (2021) Lizards of a different stripe: phylogenetics of the Pedioplanis undata species complex (Squamata, Lacertidae), with the description of two new species. Zoosystematics and Evolution 97(1): 249-272. https://doi.org/10.3897/zse.97.61351
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The lacertid genus Pedioplanis is a moderately speciose group of small-bodied, cryptically-colored lizards found in arid habitats throughout southern Africa. Previous phylogenetic work on Pedioplanis has determined its placement within the broader context of the Lacertidae, but interspecific relations within the genus remain unsettled, particularly within the P. undata species complex, a group largely endemic to Namibia. We greatly expanded taxon sampling for members of the P. undata complex and other Pedioplanis, and generated molecular sequence data from 1,937 bp of mtDNA (ND2 and cyt b) and 2,015 bp of nDNA (KIF24, PRLR, RAG-1) which were combined with sequences from GenBank resulting in a final dataset of 455 individuals. Both maximum likelihood and Bayesian analyses recover similar phylogenetic results and reveal the polyphyly of P. undata and P. inornata as presently construed. We confirm that P. husabensis is sister to the group comprising the P. undata complex plus the Angolan sister species P. huntleyi + P. haackei and demonstrate that P. benguelensis lies outside of this clade in its entirety. The complex itself comprises six species including P. undata, P. inornata, P. rubens, P. gaerdesi and two previously undescribed entities. Based on divergence date estimates, the P. undata species complex began diversifying in the late Miocene (5.3 ± 1.6 MYA) with the most recent cladogenetic events dating to the Pliocene (2.6 ± 1.0 MYA), making this assemblage relatively young compared to the genus Pedioplanis as a whole, the origin of which dates back to the mid-Miocene (13.5 ± 1.8 MYA). Using an integrative approach, we here describe Pedioplanis branchi sp. nov. and Pedioplanis mayeri sp. nov. representing northern populations previously assigned to P. inornata and P. undata, respectively. These entities were first flagged as possible new species by Berger-Dell’mour and Mayer over thirty years ago but were never formally described. The new species are supported chiefly by differences in coloration and by unique amino acid substitutions. We provide comprehensive maps depicting historical records based on museum specimens plus new records from this study for all members of the P. undata complex and P. husabensis. We suggest that climatic oscillations of the Upper Miocene and Pliocene-Pleistocene era in concert with the formation of biogeographic barriers have led to population isolation, gene flow restrictions and ultimately cladogenesis in the P. undata complex.
Biogeography, molecular phylogeny, phylogenetics, southern Africa, species description, taxonomy
The Lacertidae is a large family of Old World lizards with a center of diversity in southern Africa, particularly in xerothermic habitats (
Pedioplanis undata was originally described as a single widespread species, Lacerta undata Smith, 1838, and one year later transferred to the genus Eremias Fitzinger, 1834 by
Multiple recent molecular phylogenies have confirmed the monophyly of the P. undata species complex (including P. husabensis, as sister to all remaining species;
We present the most comprehensive phylogenetic assessment yet of the P. undata species complex in order to resolve interspecific relationships among described species, investigate the status of previously recognized unnamed lineages, and elucidate the geography of species diversification within the complex. We compiled a new and extended multi-locus dataset and reconstructed the phylogeny of the genus Pedioplanis as a whole with a greatly increased sample set for each member of the P. undata species complex throughout their ranges, particularly in Namibia.
The majority of specimens included in this study were collected by the authors, under permitted fieldwork in Namibia, South Africa and Botswana. Specimens were euthanized, fixed in 10% neutral buffered formalin, and stored in 70–75% ethanol (EtOH). Prior to fixation, tail, thigh muscle or liver tissue was preserved in 95% EtOH for subsequent DNA sequencing. Specimens have been deposited in the Museum of Comparative Zoology at Harvard University (
Genomic DNA was extracted using the Qiagen DNAeasy Kit. PCR amplification was performed on an Eppendorf Mastercycler gradient thermocycler using primer pairs obtained from published sources (see Suppl. material
Sequences were generated for 428 individuals, including all 13 currently recognized species of Pedioplanis and eight outgroup taxa (Nucras aurantiacus, N. holubi, N. tessellata, Heliobolus lugubris, Ichnotropis capensis, Meroles knoxii, M. reticulatus, M. suborbitalis). Based on recent molecular phylogenies (
Phylogenetic analyses using Maximum likelihood (ML) and Bayesian inference (BI) were performed on the CIPRES Science Gateway v3.3 (
Morphological comparisons among members of the P. undata complex were made following initial phylogenetic analysis. A diversity of mensural and meristic measures was recorded for 120 specimens including the type series of the new species described herein, and additional specimens representative of major clades revealed by the phylogenetic analyses. In order to obtain adequate sampling to capture morphological variation in each clade, we added non-genotyped adult individuals (≥ 40 mm snout–vent length) of P. undata sensu stricto (n = 6) collected from the Oanob Dam (near Rehoboth) population, and of P. rubens (n = 9) from the Klein Waterberg population, to the morphological analyses (see Appendix 1 for a complete list of specimens used for the morphological analyses). Morphological data included the following measurements in mm (for bilateral features only right side values were recorded, unless damaged): Snout–vent length (SVL) – snout tip to the anterior edge of the cloaca; body length (BL) – anterior edge of cloaca to posterior edge of collar; collar-snout length (CSL) – posterior edge of collar to snout tip; head length (HL) – posterior edge of the occipital to snout tip; maximum head width (HW); lower jaw length (JL) – anterior edge of jaw bone to tip of lower jaw; length of the fourth finger (FiL) and fourth toe (ToL); inter-limb length (IL)– length between axillary and inguinal regions; hind limb (tibia) length (HiL); forearm length (FoL) – elbow to wrist; tail length (TaL) – posterior edge of cloaca to tail tip. All measurements were collected using Mitutoyo digital calipers (to 0.1 mm). Comparative data for Angolan taxa were obtained from
Features of head and body scalation recorded were: prefrontal contact (PF); number of small granules in front of supraoculars touching frontal and prefrontal (G); number of rows of granules between supraoculars and supraciliaries (RG); number of supraciliaries (Su); interparietal-occipital contact (IO); number of infralabials (IF); number of gular scales in a straight line between the chin symphysis and median collar plate (Gu); number of subdigital lamellae on fourth toe (SuL); number of femoral pores on right leg (left if right leg was damaged or pores obscured) (Fe). Features of dorsal color and pattern were also recorded. All recorded morphological data for the type specimens are reported in the species descriptions below and listed in Tables
X-rays and Micro-computed (micro-CT) scans of specimens in the type series designated in this study were prepared at the California Academy of Sciences and Museum für Naturkunde, respectively, to obtain presacral vertebrae counts (PV). All x-ray images were taken using a Faxitron Cabinet X-ray System Model 43855C (Faxitron, Tucson, AZ, USA) at 45 kV for 60 s. Micro-CT scans were obtained using a Phoenix nanotom X-ray|s tube at 85 kV and 120 or 150 μA, generating 1440 projections with 750 ms per scan, with differing kV-settings depending on the respective specimen size. Effective voxel size, i.e., resolution in three-dimensional space, ranged from 12.8 to 14.3 μm. The cone beam reconstruction was performed using the datos|x-reconstruction software (GE Sensing & Inspection Technologies GMBH phoenix|x-ray datos|x 2.2) and the data were visualized in VG Studio Max 3.1. Micro-CT scans have been deposited on the
Due to limited sample sizes we ran our morphological analyses on a dataset combining data for adult males and females of each species; all statistical analyses were performed in R (
Allometric effects were taken into account when mensural characters were compared. We built bivariate linear models using the raw measurements of each character in relation to the respective individual’s SVL and compared the slopes of the regression lines visually using the ggplot2 package (
Final alignments of the in-group Pedioplanis taxa were as follows: ND2: 905 base pairs (429 variable, 379 parsimony informative); cyt b: 1,032 base pairs (444 variable, 363 parsimony informative); KIF24: 484 base pairs (72 variable, 50 parsimony informative); PRLR: 544 base pairs (73 variable, 46 parsimony informative); RAG-1: 987 base pairs (124 variable, 74 parsimony informative).
There were no conflicts in the topologies between the BI and ML analyses and both retrieved generally high nodal support (bootstraps – BS > 70%; posterior probabilities – PP > 0.95) throughout their respective trees. Separate analyses among the nuclear genes revealed no conflicts, though individually they provided little resolution and were thus concatenated into a single alignment. Within the concatenated nuclear tree (not shown) P. benguelensis, P. husabensis and P. rubens were found to be monophyletic with strong support (P. benguelensis: PP = 1.0, BS = 100%; P. husabensis: PP = 1.0, BS = 100%; P. rubens: PP = 0.85, BS = 100%). However, all supraspecific clades within the P. undata complex were weakly supported by our nuclear data, and relationships among them remained largely unresolved.
Separate analyses were performed on the individual and concatenated mitochondrial genes ND2 and cyt b. Each analysis resulted in a well-resolved tree and no taxonomically relevant topological conflicts were revealed. Our concatenated mitochondrial analyses (Fig.
Sampling map and phylogeny of Pedioplanis. (a.) Satellite map of Namibia depicting sampling localities for genotyped specimens of P. husabensis and the six major clades within the P. undata species complex recovered by maximum likelihood and Bayesian analysis of the concatenated mitochondrial dataset. (b, c.) Maximum likelihood phylogram depicting (b.) the interspecific phylogenetic relationships among all Pedioplanis species and (c.) all major clades within the P. undata species complex; colored triangles indicate multiple sequenced individuals; typical dorsal patterning for each member of the complex is shown based on photographs of live individuals and museum vouchers. Bootstrap values (above) and posterior probabilities (below) are provided for each major node. Satellite map of Namibia and surrounding countries created by using the Google Maps terrain map layer, which was accessed through the Free and Open Source QGIS (QGIS.org 2021) and its OpenLayers Plugin.
Within the clade containing the four recognized species of the P. undata species complex (P. undata, P. gaerdesi, P. inornata, P. rubens) we recovered a total of six highly divergent lineages (Figs
Maximum likelihood phylogeny of the Pedioplanis undata species complex inferred from the concatenation of the two mitochondrial genes ND2 and cyt b. Major geographically-structured clades are depicted for each species: (a.) P. branchi sp. nov. (yellow), P. gaerdesi (green), P. mayeri sp. nov. (teal), P. rubens (brown), (b.) P. inornata (blue) and P. undata (orange). Triangles indicate multiple sampled specimens. Locality names in bold refer to more inclusive area represented by the clade, parenthetical place names are main specific localities. Number ranges correspond to the sample numbers in Suppl. material
The final morphological dataset (adults only) contained 13 P. undata “North” (7 males, 6 females), 20 P. inornata “Central” (15 males, 5 females), 22 P. inornata “South” (15 males, 7 females), 10 P. rubens (4 males, 6 females), 21 P. gaerdesi (8 males, 13 females), and 11 P. undata “South” (2 males, 9 females). We ran Shapiro-Wilk normality tests on all meristic characters and found that only Gu data was normally distributed (W = 0.9838, p = 0.2782) and met the assumption of homogeneity of variance (Levene’s test, F = 1.8392, p = 0.113), whereas all other characters were not normally distributed: G (W = 0.95389, p = 0.0018), Su (W = 0.56256, p < 0.001), IF (W = 0.74376, p < 0.001), SuL (W = 0.95704, p = 0.0044), Fe (W = 0.93945, p < 0.001) (see Suppl. material
Using ANOVA or Kruskal-Wallis rank sum tests (and subsequently applied Wilcoxon rank sum test) we found significant differences only in the number of subdigital lamellae on the fourth toe (SuL; Kruskal-Wallis chi-squared = 11.603, p = 0.0407) and the number of femoral pores on the leg (Fe; Kruskal-Wallis chi-squared = 24.992, p < 0.001) between the species of the P. undata complex. Since none of these differences contribute meaningfully to the diagnosis of the new taxa we present the data in the Suppl. material
For the difficult to distinguish species pairs P. undata “North” and P. undata “South”, as well as P. inornata “Central” and P. inornata “South”, we assessed mensural characters in an allometric context by comparing their linear regressions (see Suppl. material
Our phylogenetic results support the existence of two highly divergent, unnamed entities within the P. undata species complex, each previously recognized as a putatively distinct, but unnamed lineage of a recognized taxon (P. undata and P. inornata). The results of the phylogenetic analyses further indicate that these lineages exhibit species-level genetic differentiation and, on this basis, we elevate the P. undata “North” clade and the P. inornata “Central” clade to full species, which we describe here using the general lineage concept of species (
(Fig.
n = 8 (all specimens are adults unless otherwise noted); three ♀:
Distinguished from P. lineoocellata, P. laticeps and P. burchelli by having 10 longitudinal ventral scale rows (vs. 12 or more). It is distinct from P. gaerdesi, P. benguelensis, P. husabensis, P. namaquensis and P. breviceps in possessing a semi-transparent lower eyelid with a brille formed by 2–4 enlarged scales (brille formed by a single scale in P. benguelensis and P. gaerdesi, lower eyelid with eight opaque scales in P. husabensis and opaque and scaly in P. breviceps and P. namaquensis). Dorsal patterning is characterized by the presence of five, usually bold dark brown to black, straight-edged dorsal stripes, distinguishing it from P. rubens (dorsum and tail uniform red-brown to brick red, lacking conspicuous markings with only a hint of a slightly brighter dorso-lateral line on each side), P. inornata, P. gaerdesi and P. branchi sp. nov. (dorsum may be light to dark gray becoming gradually more reddish towards the tail, possessing dark and/or light beige-yellowish speckling but lacking distinct longitudinal elements), P. haackei (only three dark dorsal stripes), and P. undata (dorsal striping bold or not, may be reduced with pale longitudinal elements or even a single middorsal stripe restricted to the nape). It is further distinguished from P. haackei by typically having a smaller number of granules anterior to the first supraocular (9–16 vs. 12–32), from P. huntleyi in having a larger number of granules anterior to the first supraocular (9–16 vs. 7–13), and from P. undata in possessing a greater maximum number of granular scales anterior to the supraoculars (9–16 in P. mayeri sp. nov. versus 8–13 in P. undata), and a greater maximum number of femoral pores on a single leg (12–16 in P. mayeri sp. nov. versus 11–14 in P. undata) (see Suppl. material
Body relatively slender; SVL 45.5 mm; interlimb distance 20.4 mm; femur 10.0 mm; tibia 9.8 mm; humerus 5.5 mm; forearm 5.8 mm; body length 28.9 mm from groin to collar; collar-snout length 16.1 mm; fourth finger length 5.7 mm; fourth toe length 11.1 mm; head narrow and elongated (head width 52% of head length) with narrow pointed snout (width at rear of frontonasal 2.2 mm, width at front of eye 3.8 mm); head length 11.0 mm; head width 5.7 mm; lower jaw length 8.5 mm; eye–ear distance 4.1 mm; eye–nostril distance 3.8 mm; 1.6 mm between the nostrils; original unregenerated tail 116.7 mm. Rostral semicircular, contacting nasals and supranasals; nostril surrounded by nasal, supranasal, and postnasal; nasals unraised relative to rostral and frontonasal; postnasal contacts nasal, supranasal, frontonasal, anterior loreal, and enters the nostril; nostrils circular; two loreals, anterior half the length of the posterior; two preoculars; prefrontals in median contact; frontal large, with a narrow posterior projection that contacts the frontoparietals; frontoparietals in medial contact; interparietal in contact anteriorly with both frontoparietals, laterally with the parietals, and posteriorly with the occipital; occipital partially fused with parietals at posterior margin; two supraoculars, both in contact with the frontal, preceded anteriorly by a group of 15R/16L granules, two granules in contact with prefrontal and two in contact with frontal (L); one granule in contact with prefrontal and two in contact with frontal (R); two rows of granules dividing anterior supraocular from supraciliaries; three small scales between last supraciliary and parietal; six supraciliaries on each side, anterior-most longest; lower eyelid with transparent brille formed of two larger, black-edged scales, with a row of five smaller scales below; five supralabials anterior to subocular and three supralabials posterior to subocular, on both sides; subocular bordering lip, its lower edge narrower than its upper; 6R/6L infralabials; first infralabial in contact with the second infralabial, the first chin shield, and the mental; four enlarged pairs of chin shields, the first three in median contact and enlarging progressively to the posterior; two enlarged temporals; tympanum sunken; no scales projecting significantly past margin of ear opening; enlarged narrow scale at anterodorsal margin of tympanum. 28 gular scales in a straight line between symphysis of chin shields and median collar plate; collar free, comprising 11 enlarged plates (median trapezoidal) and extending onto side of neck as a crease that terminates midway up the lateral surface; dorsal scales small, juxtaposed, granular, without keels, lateral scales becoming increasingly larger ventrally; 53 rows of granular scales around the midbody; ventral plates in 10 longitudinal and 30 transverse rows (from collar to groin); ventral scales squarish, subimbricate; single transverse row of ventrals across chest just posterior to collar longer than broad; 11 enlarged precloacal scales, irregularly sized; scales on upper surface of forearm large, smooth, and overlapping, without keels; scales on lower surface of forearm with a series of enlarged plates, at least twice width of scales on upper forearm; scales on upper surface of tibia rhombic, subimbricate and distinctly keeled, below with a series of enlarged plates; scales on upper surface of femur keeled with enlarged scales along the anterior margin; 15 femoral pores on each side; 27 subdigital lamellae under fourth toe; scales on tail uniform, obliquely rectangular in shape, and strongly keeled; 24 presacral vertebrae.
Dorsum of crown gray-tan with small speckles of varying size on head shields; dorsum of snout tinged with reddish-brown. Lateral surface of head cream-colored with minute gray speckles on loreal scales, supralabials and infralabials. Granules bordering lower eyelid window white. Color and pattern of temporal region confluent and consistent with those on trunk. Trunk dorsum with three bold black stripes each bordered on either side by whitish-cream stripes that extend to the sacrum, becoming indistinct on the tail; middorsal black stripe divided anteriorly by a whitish–cream stripe that extends from the occiput to the level of the forelimb insertion, narrowing from a width of five granular dorsal scales to two from anterior to posterior. Below the lateralmost of these pale stripes, which originates on the temporal, lies a thick darkly pigmented line to which is fused the coalescence of a series of 9R/8L irregularly sized ocelli with pale gray-blue centers comprising 6–14 granules, each surrounded by a brown to black ring. This in turn is bordered ventrally by a diffuse white line which begins at the corner of the mouth, passes through the ear and continues to the groin. Below this line the flanks transition to the immaculate pearly white of the venter. Dorsal surfaces of forelimbs mottled brown with margins of enlarged scales pale; dorsal surfaces of hind limbs medium brown, enlarged scales on preaxial surface similar to those of forelimb, postaxial surfaces bearing scattered cream-colored spots, each 1–3 granular scales in extent; palms and soles gray with scattered diffuse pinkish to orange markings. Tail light brown, densely speckled with darker markings which continue the bold lateral black stripes of the body dorsum as a pair of narrow dark brown stripes running along the medial-most keels of the tail for at least three quarters of its length.
Measurements for the type series are summarized in Table
Morphological data for Pedioplanis mayeri sp. nov. type series.
Type Status | Holotype | Paratype | Paratype | Paratype | Paratype | Paratype | Paratype | Paratype | Paratype |
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Museum No. |
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Sex | Female | Female | Female | Female | Male | Male | Male | Male | Male |
SVL (mm) | 45.5 | 40.7 | 47.0 | 43.3 | 44.0 | 51.4 | 49.2 | 43.5 | 52.7 |
TaL (mm) | 116.7 | NA (INC) | 108.5 | 105.4 | 107.3 | 124.9 | 131.8 | 96.4 | 121.5 |
PF | C | C | S | C | C | C | C | C | C |
G | 16 | 9 | 11 | 15 | 14 | 10 | 11 | 10 | 13 |
RG | 2 | 2 | 2 | 1 | 1 | 2 | 2 | 2 | 2 |
Su | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 |
IO | C | C | C | C | C | C | C | S | C |
IF | 6 | 6 | 6 | 6 | 6L/7R | 7L/6R | 6 | 6 | 6 |
Gu | 28 | 28 | 29 | 28 | 31 | 27 | 29 | 31 | 29 |
SuL | 27 | 25 | 25 | 26 | 27 | 28 | 27 | 26 | 26 |
Fe | 15 | 13 | 14 | 13 | 14 | 14 | 14 | 14 | 13 |
PV | 24 | 25 | 24 | 25 | 24 | 24 | 24 | 25 | 24 |
MB | – | – | 61 | – | 57 | 64 | 64 | 58 | – |
(Fig.
Life photographs of representative individuals of Pedioplanis mayeri sp. nov. highlighting color pattern variation within the species. (a.) Dorsal and (b.) lateral whole body images of an adult possessing bold dorsal stripes collected at the type locality (Farm Omandumba, Erongo Region, Namibia), note the row of yellow spots along the flanks; (c.) Dorsal image of an adult from the Kamanjab area depicting fainter, medium-brown dorsal stripes; (d.) An adult female collected from Gobabis (
Pattern as described above though dark stripes may fade to dark gray, yellow lateral spots may appear cream white or gray-blue, and red coloration usually present on the dorsum of the midbody and tail may become a faded orange-pink or may fade to a faint, golden-brown hue.
Pedioplanis mayeri sp. nov. is endemic to northern Namibia and occurs from south of the Kunene River and east of the Namib Desert along the eastern side of the escarpment, thence throughout the eastern Kunene Region, entering the northeastern parts of the Erongo Region and east through the Otjozondjupa Region, reaching at least as far east as Oshikango (TM17028) in the north, Gobabis (Omaheke Region) in the south-east, and Nauchas in the south. It does not enter the Kalahari dune fields, and is possibly absent from the Khomas Hochland, where it is replaced by P. undata (see Fig.
The specific epithet is a patronym formed in the genitive singular honoring our friend and colleague, the Austrian lacertid specialist Werner Mayer (1943–2015), who first recognized the distinctiveness of his namesake species and whose contributions to the study of Pedioplanis have been seminal.
Pedioplanis mayeri is widespread in northern Namibia and inhabits Tropical & Subtropical Grasslands, Savannas & Shrublands and Deserts & Xeric Shrublands biomes (following the classification of the WWF;
Habitat of Pedioplanis mayeri sp. nov. (a.) Collection site near Gobabis for
The species occurs across a wide area of Namibia in which potential threats from agriculture and mining are scattered and localized. Local populations occur in protected areas within Etosha National Park and Waterberg Plateau Park as well as in many local conservancies. Applying IUCN criteria, we consider P. mayeri to be Least Concern.
Topographic maps showing locality records for all the species of the Pedioplanis undata species complex and P. husabensis: (a.) P. husabensis (b.) P. mayeri sp. nov. (c.) P. rubens (d.) P. branchi sp. nov. (e.) P. gaerdesi (f.) P. undata (g.) P. inornata. Black dots represent museum vouchers from various museum collections, those with a white center were sequenced and included in the phylogenetic analyses. Museum voucher information was collected from the California Academy of Sciences San Francisco/USA, Carnegie Museum of Natural History Pittsburgh/USA, Ditsong National Museum Pretoria/South Africa, Iziko South African Museum Cape Town/South Africa, Museum für Naturkunde Berlin/Germany, Museum of Comparative Zoology Harvard University/USA, Museum of Vertebrate Zoology Berkeley/USA, Natural History Museum of Los Angeles County/USA, Bayworld Museum Port Elizabeth/South Africa, National Museum of Namibia Windhoek/Namibia, Zoological Research Museum Alexander Koenig Bonn/Germany, in parts via the Global Biodiversity Information Facility (GBIF; https://www.gbif.org/).
The type series of Eremias inornata Roux, 1907 comprises eight specimens collected from “Oranje-Fluß, Kl.-Namaqualand” [the Orange River, Little Namaqualand, Northern Cape, Province, South Africa]. Syntype ZMA11049 (Zoological Museum Amsterdam) was subsequently designated as the lectotype (
(Fig.
n = 7 (adults); (two ♀:
Distinguished from P. lineoocellata, P. laticeps and P. burchelli by having 10 longitudinal ventral scale rows (vs. 12 or more). It is distinct from P. benguelensis, P. gaerdesi, P. breviceps, P. namaquensis and P. husabensis in usually possessing a semi-transparent lower eyelid with a brille formed by 2–4 scales (brille formed by a single scale in P. benguelensis and P. gaerdesi, lower eyelid with eight opaque scales in P. husabensis and opaque and scaly in P. breviceps and P. namaquensis); in some rare cases P. branchi sp. nov. may possess a single transparent scale in lower eyelid, those individuals can be distinguished from P. benguelensis and P. gaerdesi by color and dorsal patterning (see below). Dorsal patterning is characterized as being uniformly gray from the mid-back towards the head with a reddish hindbody (posterior half of body) and with a series of pale to bright yellow spots or ocelli on lower flanks, distinguishing it from P. rubens (dorsum and tail uniform red-brown to brick red, lacking conspicuous markings with only a hint of a slightly brighter dorso-lateral line on each side), P. mayeri sp. nov., P. haackei, P. huntleyi, P. undata (dorsum contains bold stripes or other longitudinal elements), P. gaerdesi (never with lateral ocelli, and speckled with very small black or light dots) and P. inornata (spots on flanks are typically pale green, not yellow). It can further be distinguished from all other Pedioplanis (except P. inornata) in typically having a pair of distinct dark markings on the face, one through the eye and extending onto the supralabials directly below and one more posterior, near the corner of the mouth. The new species is significantly smaller than P. inornata (P. branchi mean adult SVL = 44.4 mm, max. 49.1 mm, versus P. inornata mean adult SVL 47.3 mm, max. 54.0 mm for specimens sampled here; to 56.0 mm elsewhere [
Body relatively slender (SVL 47.5 mm); interlimb distance 16.8 mm; femur 9.5 mm; tibia 8.7 mm; humerus 5.4 mm; forearm 5.7 mm; body length 26.9 mm from groin to collar; collar-snout length 19.3 mm; fourth finger length 4.7 mm; fourth toe length 10.4 mm; head narrow and elongated (head width 55% of head length) with slight constriction at base of rostrum and narrow, pointed snout (width at rear of frontonasal 2.2 mm, width at front of eye 4.4 mm); head length 11.8 mm; head width 6.6 mm; lower jaw length 10.2 mm; eye–ear distance 4.4 mm; eye–nostril distance 4.0 mm; 1.1 mm between the nostrils; complete original tail 92.3 mm, with epidermis missing from posterior portions. Rostral semicircular; contacting nasals; nasals in contact medially, unraised relative to rostral and frontonasal; postnasal contacts nasal, frontonasal, anterior loreal, and enters the nostril; nostrils circular in shape; two loreals, anterior loreal half the length of the posterior loreal; two preoculars; prefrontals in median contact; frontal large, with a narrow posterior projection, bordered anteriorly by the prefrontals and posteriorly by the frontoparietals; frontoparietals in broad medial contact; interparietal in contact anteriorly with both frontoparietals, laterally with the parietals, and posteriorly with the occipital; occipital trapezoidal in shape; two supraoculars, both in medial contact with the frontal and frontoparietals, preceded anteriorly by 8R/8L granules (on left side two granules in contact with prefrontal and one in contact with frontal; on right side two granules in contact with prefrontal and three in contact with frontal); single row of granules dividing anterior supraocular from supraciliaries, and double row of granules dividing posterior supraocular from supraciliaries; two small scales between last supraciliary and parietal; six supraciliaries on each side, the anteriormost longest; lower eyelid with transparent brille formed of two larger, black-edged scales, with a row of five smaller scales beneath; five supralabials anterior to subocular and three supralabials posterior to subocular, on both sides; subocular bordering the lip, its lower edge shorter than its upper; 6R/6L infralabials; first infralabial in contact with the second infralabial, the first chin shield, and the mental; four enlarged pairs of chin shields, with the first three in medial contact and the posterior-most largest; no enlarged temporals; tympanum sunk; no scales projecting significantly past margin of ear opening; enlarged narrow scale at anterodorsal margin of ear opening. 30 gular scales in a straight line between symphysis of chin shields and median collar plate; collar free, comprising nine enlarged plates (median kite-shaped, projecting posteriorly) and extending onto side of neck as a crease that terminates midway up the lateral side; dorsal scales small, juxtaposed, granular, without keels, lateral scales larger towards ventrals; 49 rows of granular scales around the midbody; ventral plates in 10 longitudinal and 31 transverse rows (from collar to groin); plates of the outermost rows squarish, ventral rows usually twice as wide as long; single transverse row of ventrals across chest just behind collar longer than broad; nine enlarged precloacal scales, irregular in shape, median ones larger; centralmost enlarged precloacal in contact with six other enlarged precloacals; scales on upper surface of forearm large, smooth, and overlapping, without keels; scales on lower surface of forearm with a series of enlarged plates, at least twice the width of scales on upper forearm; scales on upper surface of tibia rhombic, subimbricate and distinctly keeled, below with a series of enlarged plates; scales on upper surface of femur granular and smooth with enlarged scales along the anterior margin; 12R/12L femoral pores; subdigital lamellae under fourth toe 26R/28L; scales on tail obliquely rectangular in shape, and strongly keeled.
Dorsum of head gray-tan with distinct black speckles of varying size on the head shields; lateral surface of head with three bold, black vertical bars, one at the anterior margin of eye, one originating on the ventral eyelid and one just posterior to the orbit, all extending onto the supralabial scales; body dorsum uniform gray-tan with small, dense, indistinct black speckles. The flanks bear reticulate patterning and possess a single row of eight ocelli with light gray-blue spots of varying size (comprising 8–11 granules) bordered by indistinct black rings of 1–3 granules in width; black rings of adjacent ocelli either separated by 2–4 granules, or in some cases connected; venter cream; limbs pigmented above similar to dorsum, and white below; dorsum of tail with black speckling that is denser than that of the dorsum of body; tail transitions to pinkish-yellow towards the end; ventral surface of the tail is uniformly light cream.
Measurements for the type series are summarized in Table
Morphological data for Pedioplanis branchi sp. nov. type specimens.
Type Status | Holotype | Paratype | Paratype | Paratype | Paratype | Paratype | Paratype | Paratype |
---|---|---|---|---|---|---|---|---|
Museum No. |
|
ZMB89310 | ZMB89311 |
|
|
|
|
|
Sex | Male | Female | Female | Male | Male | Male | Male | Male |
SVL (mm) | 46.6 | 48 | 42.5 | 50.0 | 40.0 | 49.0 | 44.1 | 46.6 |
TaL (mm) | 92.3 | 88.4 | 111.2 | 107.0 | 99.0 | 99.0 | 94.1 | 60.9 (RGN) |
PF | C | SF | C | C | C | C | C | SF |
G | 8 | 12 | 14 | 11 | 11 | 14 | 11 | 9 |
RG | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 1 |
Su | 6 | 5 | 6 | 6 | 6 | 7 | 7 | 6 |
IO | C | C | C | C | C | C | C | C |
IF | 7 | 6 | 6 | 7 | 6 | 6 | 7 | 6 |
Gu | 30 | 30 | 26 | 30 | 26 | 30 | 32 | 28 |
SuL | 26 | 29 | 28 | 26 | 25 | 25 | 27 | 29 |
Fe | 11 | 10 | 12 | 12 | 10 | 13 | 13 | 11 |
PV | 24 | 25 | 24 | 24 | 24 | 24 | 23 | 24 |
(Fig.
Life photographs of representative individuals of Pedioplanis branchi sp. nov. highlighting color pattern variation within the species. (a.) Lateral and (b.) dorsal whole body images of an adult specimen from the Chuos Mountains (Chuosberg) (SK376.2014; not included in study), note the dense, dark speckling on the dorsum, and bold dark lateral markings. (c.) Dorsal and (d.) lateral whole body images of an adult specimen (SK402.2014; not included in study) from the northward extension of the Swakop River Canyon, note the more uniformly gray and red dorsum lacking speckling and fainter yellow spots along the flanks. Lateral (e.) head and (f.) whole body images of an adult specimen from the northward extension of the Swakop River Canyon; note the black, vertical bar beneath the lower eyelid, the bold, dark lateral markings on the body, and the distinct longitudinal row of yellow spots along the flanks.
In comparison to the life coloration, the row of spots along the flanks that appear yellow in life appear gray-blue in preserved specimens and may be conspicuous or faint, and the reddish-brown color of the posterior body and tail appears darker and more grayish.
Pedioplanis branchi sp. nov. is endemic to the Erongo Region in Namibia. Its range stretches from just south of the Swakop River in the South, where it occurs in parapatry with P. husabensis, through the pro-Namib, to the Ugab River and the Brandberg in the north and Mount Erongo and Otjimbingwe in the east, probably occurring in parapatry with P. mayeri all along its northeastern border (see Fig.
The specific epithet is a patronym formed in the genitive singular honoring our friend and colleague, the British-born South African herpetologist, William Roy Branch (1946–2018), in recognition of his many contributions to African herpetology and in remembrance of many happy trips in the field together.
Pedioplanis branchi inhabits Namibian savanna woodlands and the gravel plains and rocky outcrops in the Namib Desert (Deserts & Xeric Shrublands biome;
Habitat of Pedioplanis branchi sp. nov. (a.) Collection site for
Although P. branchi has an extent of occurrence below 20,000 km2 it occurs in an area with low human population density, generally low intensity land use, and a high proportion of suitable habitat. Populations occur in protected areas within Namib-Naukluft Park and Tsiseb Conservancy, and possibly Dorob National Park. Applying IUCN criteria we consider P. branchi to be Least Concern.
In order to resolve the systematics and biogeography of the Pedioplanis undata species complex we analyzed a new and greatly extended multi-locus molecular dataset comprising 455 samples, from all 13 currently recognized species of Pedioplanis and eight outgroup taxa. The results from our phylogenetic analyses show that interspecific relationships within the genus Pedioplanis are largely congruent with previous studies, but with several notable exceptions. We recover with strong support the phylogenetic affinities of three species that have heretofore remained problematic, P. benguelensis, P. husabensis and P. rubens. Within the P. undata species complex our results support the recognition of two highly divergent lineages and multiple instances of polyphyly.
Historically, P. benguelensis was thought to be closely related to P. namaquensis due to similarities in dorsal patterning (
We identify two instances of polyphyly within the P. undata complex. First, P. inornata as previously defined comprises two divergent lineages, one that occurs in the eastern and southern parts of Namibia, and in the Northern Cape of South Africa (= P. inornata) and another comprising individuals from central-western Namibia (= P. branchi sp. nov.). The two lineages are not each other’s closest relatives; rather, P. branchi sp. nov. is sister to P. gaerdesi. This result was corroborated by the nuclear data, in which the concatenated phylogeny recovered these clades as being distinct from one another. Interestingly, some P. branchi sp. nov. individuals possess a single (instead of two) large semi-transparent scale (“brille”) in the lower eyelid, which caused them to be identified as P. gaerdesi in the field given that this scale character is currently used to diagnose the species (
Another equally striking result is the discovery that P. undata comprises two genetically distinct and polyphyletic lineages. The first clade, P. undata “North” (= P. mayeri sp. nov.) includes individuals primarily from northern Namibia, (although a single sample was found as far south as Nauchas), and is sister to all remaining members of the P. undata species complex. The second lineage, P. undata “South” (= P. undata sensu stricto), is more deeply nested within the complex and is closely related to P. inornata, a result recovered by both the nuclear and mtDNA data.
Geographic isolation of populations through vicariance can result from various events, including both geological (formation of rivers, valleys, mountains, dunes) and climatic (drastic environmental change resulting from cooling, warming, or changes in precipitation resulting in habitat expansion or contraction). Southern Africa has experienced a complex paleoclimatic and geological past. In particular, the climatic oscillations of the Upper Miocene and the Pliocene-Pleistocene era are proposed to have been influential in the evolution and diversification of southern African fauna (e.g.
In addition, multiple potential geographical barriers have been hypothesized to be responsible for vicariance and subsequent cladogenesis. These include the Great Escarpment, the sand seas of the Namib Desert, shifting Kalahari sands, and rivers such as the Kuiseb, Zambezi, and Orange (e.g.
The current distribution ranges of members of the P. undata complex (see Fig.
During the Early Miocene conditions in southern Africa were wetter and warmer than today. Since then southern Africa has undergone stepwise cooling and drying.
The major uplift together with changes in drainage systems during less arid periods at the end of the Pliocene seems to coincide well with the split of P. inornata and P. undata, indicating that the now ephemeral Kuiseb and/or Swakop River might have been effective impediments to gene flow between these two sister taxa in the past. Today, in the east there are populations of P. undata occurring south of the mostly dry Kuiseb, indicating that gene flow between the two taxa is possible. For P. mayeri (the basal taxon of the clade) and P. gaerdesi, the escarpment has been suggested to form a geographical barrier (
The P. undata species complex has historically proven taxonomically challenging, in part due to the fact that most species have been distinguished chiefly by their body coloration and patterning (
Dorsal striping may be a plesiomorphic condition within the P. undata complex given that P. mayeri, the sister taxon to the remainder of the complex, as well as the Angolan outgroup species P. huntleyi and P. haackei, are all typically striped. The absence of dorsal striping in P. rubens, P. inornata and P. gaerdesi would suggest that stripes were lost in lineages that subsequently invaded more open habitats (further discussed below) whereas the ancestral, striped condition was retained within P. undata.
Members of the P. undata species complex are chiefly allopatrically distributed in regions of Namibia that are ecologically distinct; we suggest that apparent color variation both among and within species may be a result of differences in habitat and associated selective pressures. Uniformly and plainly colored taxa including P. branchi, P. gaerdesi, P. inornata and P. rubens all occur in arid regions where they are camouflaged on bare, sandy or rocky substrates that lack dense vegetation (
This hypothesized link between ecology and body coloration in the P. undata species complex may be further demonstrated by the pronounced intraspecific variation evident within the sister taxa P. inornata and P. undata. For example, within P. inornata, typical specimens possess a predominantly gray dorsum, however we encountered localized red morphs on red, hard-packed soils ca. 60 km west of Mariental, and dark morphs on basalt rock piles just north of the same town. Pedioplanis undata collected in northern localities that are characterized by substantial grass cover (
Taken together, our phylogenetic results and field observations strongly suggest that ecology is a significant evolutionary driver of body coloration and patterning within the P. undata species complex, as has also been demonstrated previously for e.g. P. lineoocellata (
The results of our study indicate that species diversity within Namibian Pedioplanis is greater than previously thought and that this diversity is concentrated within the P. undata species complex. These results settle the long-standing hypothesis originally put forth by
Based on present species distributions and divergence date estimates derived from previous phylogenetic studies on African lacertids (
This study highlights the need for dense geographic sampling among broadly distributed groups that have radiated recently and rapidly, as is the case for the genus Pedioplanis. Furthermore, without fine-scaled microhabitat data it is difficult to accurately assess ecological differences and to test our hypothesis of convergent evolution in this group, and we recommend future researchers prioritize these critical data.
The majority of organismal research in Namibia has so far mainly focused on the Namib Desert region in the west (
We thank the permit issuing authorities in Angola, South Africa and Namibia for allowing the collection of specimens within their respective jurisdictions. Curators and collections managers of the institutions cited in Tables
Voucher specimens used for morphological analyses.
Pedioplanis branchi sp. nov. –
Pedioplanis gaerdesi –
Pedioplanis inornata –
Pedioplanis mayeri sp. nov. –
Pedioplanis rubens –
Pedioplanis undata –
Sampling list for all specimens used in phylogenetic analyses
Data type: excel table
Explanation note: Locality information and GenBank accession numbers are provided for all tissue vouchers used in this study. We also provide the specimen ID numbers and mtDNA clade assignments for members of the Pedioplanis undata species complex that are depicted in Fig.
Mensural data for P. undata species complex specimens examined.
Data type: excel table
Explanation note: Minimum and maximum values (mm) for each species are reported for each character, see Materials and methods for character abbreviations and descriptions. Only adults were examined, and only individuals with intact tails were used to obtain tail length values (TaL); see Appendix 1 for a list of all specimens examined.
Meristic and scalation data for P. undata species complex specimens examined.
Data type: excel table
Explanation note: Abbreviations for character values are as follows: C = In Contact; S = Separated by granule; SF = Separated by frontal and frontonasal; SP = Separated by parietals. Data were collected from juvenile and adult specimens. See Materials and methods for character abbreviations and descriptions; see Appendix 1 for a list of all specimens examined.
Table S1. Primer pairs
Data type: excel table
Explanation note: Primers pairs used in this study; PCR annealing temperatures (°C) are provided.
Table S2. Bayesian partitioning schemes
Data type: excel table
Explanation note: Bayesian partitioning schemes for the concatenated mtDNA (Partition nos. 1–4) and concatenated nDNA (Partition nos. 5–8) datasets based on the results of our PartitionFinder v.2.1.1 analyses, in which best-fitting models of evolution were selected using the Bayesian Information Criterion (BIC) score.
Table S3. Summary statistics for select meristic variables for P. undata species complex
Data type: excel table
Explanation note: Summarized results of Shapiro-Wilk normality test, Levene’s test, Kruskal-Wallis rank sum test and ANOVA for selected meristic variables for adults (SVL ≥ 40 mm) of all species of the P. undata species complex. Columns show character (see Materials and Methods for abbreviations and descriptions), Shapiro-Wilk W (Shapiro_W) and corresponding p-value (Shapiro_p), Levene’s F (Levene_F) and corresponding p-value (Levene_p), Kruskal-Wallis chi-square statistics (KW_chi-squared) and corresponding p-value (KW_p), ANOVA F (ANOVA_F) and corresponding p-value (ANOVA_p) and degrees of freedom (df). Differences are considered significant with p ≤ 0.05 and significance codes are as follows: * = p < 0.5; ** = p < 0.01; *** = p < 0.001.
Table S4. Summarized results of Wilcoxon rank sum tests for the meristic characters
Data type: excel table
Explanation note: Summarized results of Wilcoxon rank sum tests for the meristic characters with significant Kruskal-Wallis test results (number of subdigital lamellae SuL and number of femoral pores on right leg Fe). All possible species pairs (species pair) for species of the P. undata species complex were tested. Columns show Wilcoxon W (Wilcox_W) and corresponding p-value (Wilcox_p) and significant differences (p ≤ 0.05) are indicated with * and significance codes are as follows: * = p < 0.5; ** = p < 0.01; *** = p < 0.001.
Figure S1. Linear relationships with 95% confidence level intervals of mensural characters between P. mayeri (= P. undata "North") and P. undata
Data type: PNG image
Explanation note: Linear relationships with 95% confidence level intervals of mensural characters with snout–vent length (SVL) for adult (SVL ≥ 40 mm) P. mayeri (= P. undata “North” sensu
Figure S2. Linear relationships with 95% confidence level intervals of mensural characters between P. branchi (= P. inornata "Central") and P. inornata
Data type: PNG image
Explanation note: Linear relationships with 95% confidence level intervals of mensural characters with snout–vent length (SVL) for adult (SVL ≥ 40 mm) P. branchi (= P. inornata “Central” sensu