Monday, July 30, 2018

[Herpetology • 2018] Conspicuously Concealed: Revision of the Arid Clade of the Gehyra variegata (Gekkonidae) Group in Western Australia Using An Integrative Molecular and Morphological Approach, with the Description of Five Cryptic Species


Figure 4: Live images of members of the arid clade of the Gehyra variegata group. 
(A) Gehyra variegata, Carey Downs, WA; (B) Gpurpurascens, Ilkurlka, WA; (E) Gehyra capensis sp. nov., Cape Range, WA; (F) G. capensis sp. nov., Cape Range, WA;
(G) 
Gehyra ocellata sp. nov., Barrow Island, WA; (H) G. pilbara, Woodie Woodie, WA 

Kealley, Doughty​, Pepper, et al., 2018. 
(photos: B. Maryan, R.J. Ellis).

Abstract 
The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds of gecko specimens of the Gehyra variegata group from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656 Gehyra individuals, largely assigned to G. variegata group members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566 Gehyra sequences from GenBank, resulting in a dataset of 1,222 specimens. Results indicated the existence of several cryptic species, from new species with diagnostic morphological characters, to cases when there were no useful characters to discriminate among genetically distinctive species. In addition, the cryptic species often showed counter-intuitive distributions, including broad sympatry among some forms and short range endemism in other cases. Two new species were on long branches in the phylogram and restricted to the northern Pilbara region: most records of the moderately sized G. incognita sp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicoline G. unguiculata sp. nov. is only known from a small area in the extreme north of the Pilbara. Three new species were on shorter branches in the phylogram and allied to G. montium. The moderately sized G. crypta sp. nov. occurs in the western and southern Pilbara and extends south through the Murchison region; this species was distinctive genetically, but with wide overlap of characters with its sister species, G. montium. Accordingly, we provide a table of diagnostic nucleotides for this species as well as for all other species treated here. Two small-bodied species occur in isolated coastal regions: G. capensis sp. nov. is restricted to the North West Cape and G. ocellata sp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA of G. crypta sp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However, G. ocellata sp. nov. was more closely related to G. capensis sp. nov. in the phylogenomic data and in morphology. Our study illustrates the benefits of combining phylogenomic data with extensive screens of mtDNA to identify large numbers of individuals to the correct cryptic species. This approach was able to provide sufficient samples with which to assess morphological variation. Furthermore, determination of geographic distributions of the new cryptic species should greatly assist with identification in the field, demonstrating the utility of sampling large numbers of specimens across wide areas.

Figure 4: Live images of members of the arid clade of the Gehyra variegata group.
(A) Gehyra variegata, Carey Downs, WA (WAM R119207; photo credit—B. Maryan); (B) Gpurpurascens, Ilkurlka, WA (B. Maryan);
(C) Gmontium, Skull Springs, WA (WAM R175332; R.J. Ellis); (D) G. montium, Port Hedland, WA (WAM R174324; P. Doughty);
(E) G. capensis sp. nov., Cape Range, WA (B. Maryan); (F) G. capensis sp. nov., Cape Range, WA (WAM R174314; R.J. Ellis);
 (G) G. ocellata sp. nov., Barrow Island, WA (R.J. Ellis); (H) G. pilbara, Woodie Woodie, WA (R.J. Ellis).

Composition of taxonomic groups within Australian Gehyra.

1. australis group (australisborroloolacatenatadubiakoirapamelarobusta)

2. *Relict species (xenopusspheniscuslazellimoritzipulingka)

3. variegata group:
 a. nana clade
(nanagirloorloogranulumkimberleyimultiporosaoccidentalisparananapluraporosapseudopunctata)

 b. Arid clade
  i. variegata species-group (variegatapilbaraminutamontiumversicolorcapensis sp. nov., crypta sp. nov., ocellata sp. nov.)
 ii. purpurascens species-group (purpurascenseinasleighensisincognita sp. nov.)
 iii. unguiculata sp. nov.
 iv. punctata

Notes:
Names used for various groups of Australian Gehyra species discussed in this and other recent papers (Ashman et al., 2018; Doughty et al., 2018).
* Species that do not fall neatly into either the australis or variegata groups, and tend to have relictual distributions.

Figure 4: Live images of members of the arid clade of the Gehyra variegata group.
(E) G. capensis sp. nov., Cape Range, WA (B. Maryan); (F) G. capensis sp. nov., Cape Range, WA (WAM R174314; R.J. Ellis); 
(G) 
G. ocellata sp. nov., Barrow Island, WA (R.J. Ellis); (H) G. pilbara, Woodie Woodie, WA (R.J. Ellis).

Gehyra capensis sp. nov.
North West Cape Gehyra
variegata B1 of Ashman et al. (2018)

Diagnosis. A small-bodied (to 46.0 mm SVL) species with a relatively long snout, internarial usually (72%) present, lower postnasal larger than upper, two pairs of chin shields, second infralabial notched by parinfralabial scales, usually six (occasionally seven) subdigital lamellae on the fourth toe and males with 9–12 (mean 10.8) pre-cloacal pores. Background colour pinkish-grey with dark brown irregularly shaped spots or bars with numerous smaller pale white spots not in contact with dark markings, canthal, loreal and temporal stripes on head present (no post-orbital stripes) and ventrum not stippled. Genetically diagnosed from other arid clade members by the ND2 sites in Table 3.
....

Distribution. Restricted to the North West Cape of WA (Fig. 1B).

Habitat and ecology. Recorded from spinifex and low shrubs on limestone rocks. Also encountered under logs and sheets of tin on the ground, and on human-made structures indicating a penchant for climbing behaviour.

Etymology. The specific name refers to the North West Cape of WA to which this species is restricted.


Gehyra crypta sp. nov.
Western Cryptic Gehyra
Clade 3 or III of Sistrom, Donnellan & Hutchinson (2013)
variegataB3 of Ashman et al. (2018)

Diagnosis. A moderately sized (to 56.5 mm SVL) species with moderately short snout, internarial usually (80%) present, lower and upper postnasals of similar size, two pairs of chin shields, second or third infralabial notched by parinfralabial scales, usually six or seven (rarely eight) subdigital lamellae on the fourth toe and males with 10–16 (mean 12.4) pre-cloacal pores. In preservative, light grey to dark brown with highly variable pattern: from isolated dark and pale bars to dark network with white spots to patternless, head stripes present but with lower post-orbital stripe at most a spot and ventrum moderately to heavily stippled. Genetically diagnosed from other arid clade members (except G. ocellata sp. nov.) by the ND2 sites in Table 3.

Distribution. Most records are from the southern and western Pilbara, with the northernmost records from the Burrup Peninsula, then inland through Millstream–Chichester National Park through the Hamersley Range to 50 km west of Newman. In the mid-west and WA Goldfields there are scattered genotyped records inland, away from the west coast, through the Gascoyne and Murchison bioregions, with the southernmost records from 150 km north of Kalgoorlie and the easternmost record near Laverton (see Fig. 1B).

Habitat and ecology. Possibly generalist habits. Collected from mulga woodlands and acacia shrubs, from under logs, granite and tin on hard soils. Also observed climbing on vertical surfaces of human-made structures and sheltering under bark on trees.

Etymology. The species epithet is derived from the Greek kruptos, meaning ‘hidden.’ The name alludes to this species similarity to other species in the arid clade of the G. variegata group. Used as an adjective.


Gehyra ocellata sp. nov.
Pilbara Island Gehyra
variegataB2 of Ashman et al. (2018)

Diagnosis. A small-bodied (to 49.0 mm SVL) species with moderately short snout, internarial absent or present, lower postnasal larger than upper, two pairs of chin shields, second infralabial notched by parinfralabial scales, usually six (occasionally seven) subdigital lamellae on the fourth toe and males with 10–12 (mean 11.1) pre-cloacal pores. Background colour light to medium reddish-brown with numerous pale spots with fewer brown irregular markings, head stripes poorly defined or absent and ventrum with little or no stippling. Genetically diagnosed from other arid clade members (except G. crypta sp. nov.) by the ND2 sites in Table 3.

Distribution. Restricted to islands off the Pilbara coast near Karratha, including Barrow, Varanus, Trimouille and Hermite (Fig. 1B).

Habitat and ecology. Observed to inhabit termite mounds (P. Kendrick, R. J. Teale, 2018, personal communication). Otherwise poorly known, as most records are associated with oil and gas buildings and structures. Several records mention ‘under limestone slab.’

Etymology. The species epithet ocellata (New Latin) refers to the spotted appearance of this species. Used as an adjective.


Figure 4: Live images of members of the arid clade of the Gehyra variegata group. (A) Gehyra variegata, Carey Downs, WA (WAM R119207; photo credit—B. Maryan); (B) G. purpurascens, Ilkurlka, WA (B. Maryan); (C) G. montium, Skull Springs, WA (WAM R175332; R.J. Ellis); (D) G. montium, Port Hedland, WA (WAM R174324; P. Doughty)

Gehyra incognita sp. nov.
Northern Pilbara Cryptic Gehyra
variegataC2 of Ashman et al. (2018)

Diagnosis. A moderately sized (to 52.0 mm SVL) species with moderately short snout, internarial present or absent, lower postnasal larger or equal to upper, two pairs of chin shields, second infralabial notched by parinfralabial scales, usually six (rarely five or seven) subdigital lamellae on the fourth toe and males with 10–16 (mean 12.0) pre-cloacal pores. In preservative, background colour medium grey to dark brown with poorly contrasting pattern of small dark and pale spots occasionally forming bars or networks, well-defined head stripes and ventrum heavily stippled. Genetically diagnosed from other arid clade members by the ND2 sites in Table 3.
....

Distribution. Most records are from genotyped individuals that occur near the Pilbara coast and have been collected along the Great Northern Highway. From 40 km east of Roebourne to Whim Creek and to Port Hedland area. Three inland isolated locations: Millstream–Chichester National Park, Woodstock–Abydos Protected Reserve (formerly Station; with several specimens genotyped) and from 40 km north of Marble Bar (see Fig. 1C).

Habitat and ecology. Likely arboreal. Habitat notes for quadrats that used pitfall traps for the Pilbara Biodiversity Survey (McKenzie, van Leeuwen & Pinder, 2009) mention tall acacia shrubs over Triodia, and substrates that included floodplain, clayey or silty sand and red sandy loam. The only other habitat notes from collectors are two records from Triodia plains, with no mention of rocky habitats.

Etymology. The specific name is derived from the Latin incognitus meaning ‘unknown,’ in reference to the heretofore complete ignorance of this species’ existence prior to genetic analyses. Used as an adjective.


Gehyra unguiculata sp. nov.
Crescent-marked Pilbara Gehyra
variegataC1 of Ashman et al. (2018)

Diagnosis. A small-bodied (to 39.0 mm SVL) species with moderately short snout, internarial present (67%) or absent (33%), lower postnasal larger or equal to upper, two pairs of chin shields, second infralabial notched by parinfralabial scales, usually six (occasionally seven) subdigital lamellae on the fourth toe and males with 11–13 (mean 12.3) pre-cloacal pores. In preservative, background colour light tan to medium brown with crescent-shaped dark brown bars with pale spots posteriorly, crown with pale white spots, usually poorly defined head stripes and ventrum with only light stippling towards lateral edges. Genetically diagnosed from other arid clade members by the ND2 sites presented in Table 3.
....

Distribution. Only known from two locations 30 km apart in the north-eastern Pilbara near Shay Gap, north of the De Grey River (Fig. 1C).

Habitat and ecology. Several specimens were captured in pitfall traps at sites PHYC03 and PHYC07 as part of the Pilbara Biodiversity Survey (McKenzie, van Leeuwen & Pinder, 2009). Descriptions for these sites were of scree on or near granite outcrops or hills of basalt.

Etymology. Unguiculata is Latin (diminutive) for fingernail (or claw) and refers to the resemblance of the dorsal pattern elements of this species to small fingernails. Used as an adjective.


Conclusions:
The systematics of Gehyra is intrinsically difficult owing to their conservative form, ability to shift habitat preferences from trees to rocks (Ashman et al., 2018), rapid evolution of body size (Doughty et al., 2012; Sistrom et al., 2012), a large specimen burden, few photographs in life and colours and pattern lost rapidly in preservative, among others. We generated relatively short sequences of the ND2 mtDNA gene for over 650 specimens, combining these with previously genotyped specimens and examining hundreds of specimens for morphology. We were able to make progress by combining these data with previous phylogenomic work that included hundreds of nDNA loci and that firmly established the existence of cryptic species, but based on few specimens. This combined approach is especially suited for cryptic species, as a good understanding of the geographical and morphological limits of cryptic species requires examination of many specimens over a wide area. The combined approach we advocate here culminated in the description of five new species, and clarified the distributions of previously described species as well.

Although great progress has been made on this group taxonomically, there is still further work to be done. Owing to the difficulty of describing these new species, it is clear that photographs in life are an essential part of Gehyra specimen preparation because they capture the patterning, a key component of the phenotype, and should be routinely taken when collecting them. Genetic samples (e.g. tail tip in ethanol) of Gehyra taken in the field are also essential to determine which species occurs in a specific location, especially where two or more cryptic forms overlap. Both these technologies (digital photography and genetic analyses) were not available only several decades ago, and images and tissue samples should be routinely collected by field workers today. Refinement of the diagnoses and descriptions beyond that presented here based on new phenotypic and genetic information are welcome, and may even reveal further cryptic forms within this difficult group.


Luke Kealley, Paul Doughty​, Mitzy Pepper, J. Scott Keogh, Mia Hillyer and Joel Huey. 2018. Conspicuously Concealed: Revision of the Arid Clade of the Gehyra variegata (Gekkonidae) Group in Western Australia Using An Integrative Molecular and Morphological Approach, with the Description of Five Cryptic Species. PeerJ. 6:e5334.  DOI:  10.7717/peerj.5334

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