Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cinctahas close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the late Miocene.

1. Introduction

Since the Miocene, arid climates have expanded and intensified across the Southern Hemisphere [1–3]. In response, pre-existing mesic lineages have adapted, persisted in evolutionary refugia or become extinct [4–6]. Aridification has been particularly intense and widespread in Australia, and the extant biota of the vast and continuous Australian arid zone (AAZ) displays a strong signature of climate-driven diversification and biological turnover since the Miocene [2,5,7,8]. Even lineages which have radiated within the arid zone and are now widespread, are hypothesized to have contracted to climatic refugia during hyper-arid glacial maxima [5]. However, there are a number of geologically distinctive and stable habitats within the AAZ that are believed to have functioned as evolutionary refugia for mesic-adapted taxa through the expansion of severe aridity [9]. Especially prominent are blocks of geologically stable and ancient upland country and rocky ranges with associated clusters of endemic lineages or isolated populations, including (from west to east) the Pilbara, Central Ranges, MacDonnell Ranges, Flinders Ranges and Selwyn Ranges [5,10–12].

Phylogenetic investigation of putative relict taxa endemic to ranges in arid Australia provides opportunities to understand how and when major environmental changes shaped biotic turnover across central Australia, and also assess what factors may have predisposed lineages to long persistence [11,13–15]. Recent palaeo-climatic analyses have provided compelling evidence that the overall trajectory towards increasing aridity across the Southern Hemisphere (and especially Australia) since the Late Miocene was punctuated by a sustained warm mesic interval during the early Pliocene [16]. This suggests two broad timeframes of origin for relictual taxa: (i) isolation by Miocene aridification and predating the Pliocene mesic period, or (ii) wide distributions during the warm-wet Pliocene, with subsequent contraction and isolation during the cool-dry Pleistocene. The first hypothesis predicts divergences from sister lineages that date back well into the Miocene (more than 5 Ma), while the latter predicts more recent divergences (less than 5 Ma).

The MacDonnell Ranges Bioregion (MRB) lies right at heart of the vast AAZ, is particularly isolated from the ameliorating climatic influences of the oceans, and has some of the highest levels of localized plant and animal endemism in the AAZ [17–19]. Two additional upland rocky regions nearby, the Central Ranges Bioregion (CRB) to the south, and the poorly known Murchison Davenport Ranges Bioregion (MDRB) to the northeast also have isolated and putatively relictual taxa. We hereafter refer to these systems collectively as the ‘Central Uplands’. While it was long assumed that many Central Uplands endemics are ancient mesic relicts from an initial onset of aridity during the Miocene [9,20], recent research, especially on plants, has supported more recent Plio-Pleistocene range contraction or even anthropogenic dispersal [15,21].

Here, we build on recent analyses of a lineage of Australian geckos with Gondwanan ancestry (the velvet geckos: Oedura) [12,14,22] in order to assess the diversity and origins of isolated populations in the Australian Central Uplands. Currently only one taxon (Oedura cincta), relatively closely related (estimated Pliocene divergences) to populations of Oedura occurring elsewhere in the eastern AAZ, is recognized [22]. However, a morphologically distinctive population of Oedura from the southern portion of the MRB has been noted since the 1970s [23]. Recent targeted fieldwork has provided the first genetic samples of this population. Using these samples, we here test: (i) whether these populations are conspecific with Oedura cincta elsewhere in the Central Uplands, and (ii) assess whether the divergence of different populations of Oedura in the Central Uplands is likely to post- or pre-date the Pliocene mesic interval. To place patterns of divergence within Oedura in a broader context, and to facilitate further work on Central Uplands endemism, we also present a summary of available information on the distribution, ecology, divergence timeframes and phylogenetic relationships of all known endemic or isolated vertebrate taxa and populations.

2. Material and methods

2.1. Molecular analyses

New tissue samples of Oedura from the Australian arid biome were accessed from recently collected material stored in Australian National University (CCM), The Museum and Art Gallery of the Northern Territory (NTM) and the South Australian Museum (SAMA). Regions of one mitochondrial gene (ND2–all specimens) and two nuclear genes (Phosducin and RAG-1, selected specimens) were amplified following protocols presented in by Oliver et al. [14] (see further information in the electronic supplementary material, Methods). Our final dataset included sequences from 30 new samples of Oedura from arid central and eastern Australia, which were aligned with publicly available data from other Oedura and related gecko genera ([14]; electronic supplementary material, table S1). The final dataset comprised up to 912 bp of RAG-1, 393 bp Phosducin and 846 bp of the mitochondrial ND2 gene.

Phylogenetic relationships were estimated using standard maximum-likelihood (RAxML v. 8.2.4: [24]) and Bayesian (BEAST v. 1.8.0: [25]) analyses implemented on the CIPRES Science Gateway v. 3.1 for online phylogenetic analysis (https://www.phylo.org). Partitioning strategies followed recent studies of Oedura [12], splitting mitochondrial data by codon, while the nuclear data were partitioned into first and second codon, and third codons. Maximum-likelihood analyses were run using the default settings for RAxML on the CIPRES portal using the GTR CAT model of sequence evolution [26]. For Bayesian analyses, we used the GTR + G model for mitochondrial data, and the HKY + G model for nuclear partitions. Final MCMC analyses were run for 20 million generations (with a burn-in of 20%), and parameter estimation and branch lengths were unlinked across partitions.

Dating analyses (BEAST v. 1.8.0; [25]) focused on a reduced dataset comprised of both nuclear and mitochondrial sequence data for single exemplars of species, candidate species and operational taxonomic units (OTUs) of Oedura, in addition to outgroups spanning the gecko subfamily Diplodactylidae (electronic supplementary material, table S1). As outlined elsewhere, fossil or biogeographic calibrations that provide meaningful age constraints for the pygopodoid geckos are unavailable [27]. Thus, we applied two broad normally distributed secondary age priors for basal divergence events in the Diplodactylidae that are consistent with three independent fossil-calibrated studies [14,28,29], the Core Diplodactylidae (mean 35.0 Ma (6.0 s.d.)) and the New Caledonian Pseudothecadactylus clade (43.0 Ma (9.0 s.d.)). For all dating analyses, we used the Yule speciation prior (appropriate and widely used for relatively divergent lineages). Owing to potential issues when combining saturated mitochondrial data with deep calibrations (even after third codons have been removed) [13,30], we undertook dating analyses on both the combined dataset with third codons removed, and the nuclear alignment alone. For each data alignment, we also ran both uncorrelated-lognormal and strict clock models and compared model likelihoods by comparing AICM values as implemented in Tracer v. 1.6 [31]. In the combined dataset, the uncorrelated-lognormal model was favoured (156.2 units lower), while in the nuclear dataset the clock model was favoured (240.6 likelihood units lower).

2.2. Morphology

We examined material (including type material) held in the following institutions: Australian Museum (AMS), Museum Victoria (NMV), NTM, Queensland Museum (QM), SAMA and Western Australian Museum (WAM) (electronic supplementary material, Appendix S1). Measurement protocols and acronyms (see electronic supplementary material) largely follow those outlined elsewhere [22,32].

Statistical analyses were performed in R [33]. All mensural variables were log transformed and we inspected all transformed variables for heteroscedasticity, normality and influential observations using boxplots and diagnostic plots in R. Body and head measurements were corrected for body size by regressing against principle component 1 from an initial principle components analysis (PCA) to account for possible non-allometric growth [34]. Analyses of tail morphology were restricted to specimens with original tails and tail measurements were standardized against snout-to-vent length (SVL).

We initially used PCA of the size-corrected body and head length data to examine how distinctive populations were in multivariate space. These analyses did not reduce the number of variables required to explain variation, with the first three components only explaining 38% of variation, and are therefore not considered further.

For subsequent univariate analyses, we used one-way ANOVA to test for overall differences in morphology between four genetically and geographically divergent lineages of Oedura in the AAZ (Oedura fimbria, two mtDNA lineages of Oedura cincta and Oedura sp.). For mensural variables where there was an overall difference (p ≤ 0.05), we ran pairwise t-test comparisons (Bonferroni corrected) between each population.

2.3. Biogeographic data

We synthesized distribution records (mainly from the Atlas of Living Australia [35]) and phylogenetic data for all apparently endemic or isolated vertebrate taxa and populations from all three Central Uplands Bioregions (MRB, CRB, MDRB). Where available, we noted the estimated timeframes of divergence between endemics and nearest extant relatives occurring elsewhere in Australia. Given the wide error bars associated with molecular dating, we chose to focus on broad eras: mid-Miocene (more than 10 Ma), late Miocene (approx. 10–5.3 Ma), Pliocene (5.3–2.5 Ma) and Pleistocene (less than 2.5 Ma). We also noted the broad ecological guild of endemic taxa or populations (aquatic (i.e. dependent on water to breed), arboreal, saxicoline (with adaptations for climbing in rocky habitats), scansorial, terrestrial or fossorial), whether endemics are allopatric from known or putative sister lineages, the ecology of nearest relatives (as above), and the biome of nearest relatives (arid, temperate and monsoonal).

3. Results

3.1. Molecular diversity of Central Uplands velvet geckos

Genetic analyses of Oedura identified two highly divergent and distantly related lineages within Central Uplands: (i) the recognized Oedura cincta (central lineage) from the granitic, quartzite, limestone and sandstone rocks of the Meerenie, Chewings and Heavitree Ranges in the north of the MRB, and (ii) a highly divergent unnamed lineage (Oedura n. sp.) from the Mereenie sandstones of the James Range and surrounding systems in the south of the MRB (figure 1).

Analyses based on the combined nuclear and mitochondrial alignment (third codons removed) produced older date estimates for divergence events below the calibration prior (all taxa in the main Australian radiation of diplodactylid geckos, including both lineages of Central Uplands Oedura) (electronic supplementary material, table S2). We interpret this as most probably an artefact of combining mitochondrial data with deep calibration nodes, and focus on date estimates from the nuclear data only. However, we also emphasize that all analyses broadly support the contention that the divergence of isolated populations of Oedura cincta occurred through the Plio-Pleistocene, while in contrast Oedura n. sp. is a much more divergent relict dating back to the early, mid- or even late Miocene.

Dating analyses, using the preferred combination of nuclear data and the correlated lognormal model, estimated very late Miocene to early Pliocene divergence of central populations of Oedura cincta from relatives now living in inland eastern Australia (approx. 4.3 Ma (2.1–6.8)). By contrast, Oedura sp. has no strongly supported sister taxon (although it did tend to associate with an assemblage of taxa from eastern Australia in both mitochondrial and nuclear phylogenies) and is estimated to have diverged from all living congeners well into the Miocene (approx. 11.6 Ma (8.1–15.9)).

Tamura–Nei distances [36] estimated using the ND2 alignment within well-sampled and widespread clades within the MRB were relatively low (Oedura cincta mean 0.007 (0.000–0.017); Oedura n. sp. 0.019 (0.000–0.035)). However, three moderately divergent mitochondrial lineages of Oedura cincta were identified in the greater Central Uplands region (mean inter-clade divergences 0.051–0.061); one widespread throughout the eastern and central MRB, one from a single site in the mid-north of the MRB, and an apparently isolated lineage in the ranges at the southern edge of the Tanami Desert (outside the MRB) (figure 2).

3.2. Morphological analyses

Univariate analyses of morphology revealed consistent differences between Oedura n. sp. and other Oedura in the AAZ (figure 3a–d). It has a flatter head (compared with all other lineages, p ≤ 0.001), longer tail (compared with all other lineages, p ≤ 0.05), and flatter tail (compared with O. cincta ‘central’ and O. fimbria, p ≤ 0.01; compared with O. cincta ‘eastern’, p ≤ 0.001) (figure 3a,b,d). Oedura n. sp. also has a narrower tail than the other lineages, though this was only statistically significant when compared with O. cincta ‘eastern’ (p ≤ 0.01) (figure 3c). Variation in body condition (tails appear to become very thin in times of resource stress in all taxa) may explain the lack of statistical difference in tail width. No other meristic characters consistently differentiated Oedura n. sp. from sampled populations in the Oedura marmorata complex in the AAZ. A summary of all measurements for AAZ Oedura is provided in electronic supplementary material, table S3.

Morphological analyses also revealed additional diagnostic differences in the scalation and coloration of Oedura n. sp., in particular it is characterized by much smaller scales across the body (maximum diameter less than versus greater than 0.5 mm) (figure 3e,f), and the absence of strong canthal or postorbital striping (figure 4).

3.3. Systematics

The synonymy of the Oedura marmorata complex has recently been considered elsewhere [22]. Two names have been applied to populations from the Central Uplands, but are not applicable to new taxon. Oedura greeri Wells & Wellington [37] (holotype: AMS R87677, Mt Doreen) was described without diagnosis and is regarded as a nomen nudum [38]. Oedura derelicta Wells & Wellington [37] (holotype: NTM11413) is described based on a specimen from Jessie Gap close to Alice Springs and is currently a synonym of Oedura cincta.

Oedura luritja n. sp. (Figures 3f and 4a–d).

Mereenie velvet gecko

3.3.1. Holotype

NTM R37528, field number CCM5974, adult male with regrown tail, and liver samples stored in ethanol.

3.3.2. Type locality

Gorge 300 m east of north end of Boggy Hole (−24.13455, 132.86574), Finke Gorge National Park, Northern Territory, collected 5 October 2015 by P.J.M. and P.M.O.

3.3.3. Paratypes

All from Northern Territory (n = 11). NTM R37529 (CCM5975) near Boggy Hole (−24.1351, 132.86351), Finke Gorge National Park, collected 5 October 2015; NTM R37531 (CCM5979) Palm Creek (−24.05449, 132.74246), Finke Gorge National Park; NTM R37530 (CCM5978) Palm Creek (−24.0584, 132.76151), Finke Gorge National Park, collected 6 October 2015; AMS R52143 Kings Canyon (−24.27, 131.57), Watarka National Park, collected 28 July 1975; AMS R52144–50 Reedy Springs (−24.30, 131.58), Watarka National Park, collected 28 July 1975.

3.3.4. Referred material

All from Northern Territory. Specimens (n = 14): AMS R24662–71, NTM33811 Reedy Ck, George Gill Range (−24.28, 131.60); SAMA R65915, Rainbow Rocks (−24.3342, 133.6353); NTM R20681, Finke Gorge National Park (−23.95, 132.77); QMJ52883, Hermannsburg (−23.95, 132.77); AMS R52154, ‘47 mi sw of Alice Springs' (−24.27, 133.47). Tissue samples only (n = 6): CCM5973, Finke Gorge National Park (−24.13455S, 132.86574E); CCM5976, Finke Gorge National Park (−24.0584, 132.76151); CCM5977, Finke Gorge National Park (−24.05449, 132.74246); CCM6227, Kings Canyon (−24.25576, 131.57649), Watarrka National Park, collected 11 February 2015; CCM2228, Kings Canyon (−24.24966, 131.57366), Watarrka NP, collected 25 February 2015; CCM6229, Kathleen Springs (−24.33941, 131.68045), Watarrka NP, collected 26 February 2015.

3.3.5. Etymology

Luritja is a collective name for people speaking several dialects of the Aboriginal Western Desert language. The western parts of the distribution of Oedura luritja(including Watarrka National Park) are in Luritja lands. Luritja is also believed to be derived from the Arrernte word ‘Ulerenye’ meaning foreigner or stranger, and is therefore further appropriate for such a deeply divergent lineage. Used as a noun in apposition.

3.3.6. Diagnosis

A moderately large (to 99 mm SVL) species of Oedura with a moderately wide (HW/SVL 0.17–0.20) and flat head (HD/SVL 0.072–0.091), tail moderately long (original TL/SVL 0.65–0.87), narrow (TW/SVL 0.07–0.11), distinctly narrower than head and body and tapering gradually to a tip, rostral less than 50% divided, postcloacal spur usually single (22 out of 23 specimens), 10–16 precloacal pores in adult males, dorsal scales small (less than 0.5 mm in diameter), head brown with light flecking but with no trace of a light canthal stripe or dark-brown postorbital or nuchal stripes, and dorsal coloration of adults usually including five to six moderately well-defined light bands or transverse blotches (yellow in life) on a purplish brown background.

3.3.7. Particulars of holotype

Adult male with regrown tail (figure 4a). Quantitative measurements in millimetres: SVL 97.0, HW 18.7, HD 8.2, HL 22.9, EN 8.3, IN 3.6, IO 7.4, EYE 5.4, TrK 43.1, ArmL 13.0, LegL 14.6, 3FW 2.8, 3TW 3.2, TL 80, TW 10, TD 6.7. Scale counts: SuL 12 (10), InF 12, CS 1/1, 3FL 8, 3TL 9, precloacal pores 11 (divided medially by 2 poreless scales).

3.3.8. Description

A large (to 99 mm SVL) and moderately elongate Oedura (Trk/SVL 0.43–0.50); head moderately wide (HW/SVL 0.17–0.20) and flat (HD/SVL 0.072–0.091). Rostral 20–50% divided, bordered dorsally by two nasals, nasals bordered dorsally by two relatively small supranasals and 0–3 (mode 3) small intervening scales. Supralabials 10–12 to midpoint of eye, 12–15 in total; infralabials 11–15. Forelimbs and hindlimbs of moderate length (FA/SVL 0.12–0.14, TA/SVL 0.13–0.16). Subdigital lamellae moderately expanded and prominent, 7–8 under third finger, 8–9 under third toe. Distal lamellae divided, proximal lamellae undivided. Apical lamellae on terminal scansors separated from more proximal pairs. Lamellae series on fingers 2–5 and toes 2–5 flared at midpoint, at most equal in width to terminal scansors.

Original tail moderately long (TL/SVL 0.65–0.87), narrow (TW/TL 0.10– 0.15) and depressed in cross-section, tapering gradually to tip and with a slight ventral groove. Relative width and depth varies greatly depending on body condition. Caudal scalation homogeneous. Fully regrown tails similar length (TL/SVL 0.58–0.78) and width (TW/TL 0.11–0.16) to original tails.

In preservative, base coloration of dorsum dark purplish brown, generally with 5–6 distinct pale buff relatively straight and clearly defined transverse dorsal bands, or occasionally transverse series of blotches. Extensive further light buff flecking usually present between the bands, and elsewhere on the dorsal and lateral surfaces of the head, torso and limbs; light and brown pigmentation on head not forming clear lines or stripes. Two paratypes (AMS R52145 and AMS R52148) have strongly defined bands, lack extensive light flecking and have unusually large light blotches on the head and lateral edges of torso, and a single adult specimen (AMS R52143) lacks any clear dorsal bands. Venter plain light buff, with faint brownish tinge around the terminal lamellae and occasionally fine brown maculations around the infralabials. Original tail with 7–8 indistinct light bands on a brown background. Regrown tails brown with extensive and variable light flecking that does not form a distinct pattern.

In life, the basic pattern and coloration of individuals matches those of preserved specimens, however, the darker regions are purplish during the day, silvery grey at night, and light regions tend to be relatively bright yellow (figure 4a,b). Iris very dark brown (figure 4c).

Juveniles with simpler pattern of clear light transverse bands (and occasionally lateral blotches) on a plain dark-brown background, with light and dark bands becoming increasingly indistinct with size (figure 4d).