Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.This work has been supported by Australian Research Council grants to MJP (DP07745015) and MB (FT0991741). The website for the funder is www.arc.gov.au. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Diversification of New Zealand weta (Orthoptera: Ensifera: Anostostomatidae) and their relationships in Australasia

New Zealand taxa from the Orthopteran family Anostostomatidae have been shown to consist of three broad groups, Hemiandrus (ground weta), Anisoura/Motuweta (tusked weta) and Hemideina–Deinacrida (tree–giant weta). The family is also present in Australia and New Caledonia, the nearest large land masses to New Zealand. All genera are endemic to their respective countries except Hemiandrus that occurs in New Zealand and Australia. We used nuclear and mitochondrial DNA sequence data to study within genera and among species-level genetic diversity within New Zealand and to examine phylogenetic relationships of taxa in Australasia. We found the Anostostomatidae to be monophyletic within Ensifera, and justifiably distinguished from the Stenopelmatidae among which they were formerly placed. However, the New Zealand Anostostomatidae are not monophyletic with respect to Australian and New Caledonian species in our analyses. Two of the New Zealand groups have closer allies in Australia and one in New Caledonia. We carried out maximum-likelihood and Bayesian analyses to reveal several well supported subgroupings. Our analysis included the most extensive sampling to date of Hemiandrus species and indicate that Australian and New Zealand Hemiandrus are not monophyletic. We used molecular dating approaches to test the plausibility of alternative biogeographic hypotheses for the origin of the New Zealand anostostomatid fauna and found support for divergence of the main clades at, or shortly after, Gondwanan break-up, and dispersal across the Tasman much more recently

FIGURE 5 in Systematics of a small Gehyra (Squamata: Gekkonidae) from the Einasleigh Uplands, Queensland: description of a new range restricted species

FIGURE 5. Gehyra einasleighensis sp. nov. in life. Top: dark patterned adult specimen from 6 km south-east of Petford (CCM5160); bottom: golden patterned adult specimen from vicinity of Cobbold Gorge Village (CCM5144) (photographs—C. C. Moritz). Neither individual was taken as a voucher specimen.Published as part of Bourke, Gayleen, Pratt, Renae C., Vanderduys, Eric & Moritz, Craig, 2017, Systematics of a small Gehyra (Squamata: Gekkonidae) from the Einasleigh Uplands, Queensland: description of a new range restricted species, pp. 85-99 in Zootaxa 4231 (1) on page 92, DOI: 10.11646/zootaxa.4231.1.5, http://zenodo.org/record/29363

Systematics of small Gehyra (Squamata: Gekkonidae) of the southern Kimberley, Western Australia: redescription of G. kimberleyi Börner & Schüttler, 1983 and description of a new restricted range species

Oliver, Paul M., Bourke, Gayleen, Pratt, Renae C., Doughty, Paul, Moritz, Craig (2016): Systematics of small Gehyra (Squamata: Gekkonidae) of the southern Kimberley, Western Australia: redescription of G. kimberleyi Börner & Schüttler, 1983 and description of a new restricted range species. Zootaxa 4107 (1): 49-64, DOI: 10.11646/zootaxa.4107.1.

On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

Abstract Background Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome. Results Using a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred. Conclusions In climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain

Approximately unbiased (AU) test results.

<p>Nuclear sequences are partitioned into protein codon positions and mitochondrial sequences are partitioned into protein codon positions and RNA stems and loops.</p><p>Comparisons (A) – (D) employ Mt₁₆ and Nuc₁₇. Comparison (E) employs Mt₁₇.</p> ˆ<p>Allowing <i>W. bicolor</i> and <i>M. irma</i> to float unconstrained on the tree</p>#<p>Not including <i>M. irma</i>, which is favoured as sister to <i>M. robustus</i> on the mt data.</p

Gehyra paranana Doughty & Bourke & Tedeschi & Pratt & Oliver & Palmer & Moritz 2018, sp. nov.

&lt;i&gt;Gehyra paranana&lt;/i&gt; sp. nov. Bourke, Doughty, Tedeschi, Oliver &amp; Moritz &lt;p&gt;Litchfield spotted gecko&lt;/p&gt; &lt;p&gt;(lineage nana 3)&lt;/p&gt; &lt;p&gt;Figs. 5, 8, 9&lt;/p&gt; &lt;p&gt; &lt;b&gt;Holotype.&lt;/b&gt; NTM R37057, an adult female collected from Dorat Road, Robin Falls area, Northern Territory (13.35278&deg;S; 131.13361&deg;E), on 21 September 2013 by P.M. Oliver, P. Skipwith and M. Hammer.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Paratypes (12).&lt;/b&gt; Northern Territory: NTM R20246 (male), Butterfly Gorge, 6 km east of Daly River crossing (13.73333&deg;S; 130.73333&deg;E); NTM R37831 (field# CCM0651) and NTM R37832 (CCM0652) (females), Bullo River Station (15.65862&deg;S; 129.65944&deg;E); NTM R36578 and NTM R36579 (females), Bullo River Station (15.65766&deg;S; 129.65933&deg;E); NTM R36554 (male), Gurrandalng camp, Keep River National Park (15.87516&deg;S; 129.051&deg;E); NTM R37056 (male), Dorat Road, Robin Falls area (13.35278&deg;S; 131.13361&deg;E); NTM R37833 (CCM2881) (female), NTM R37834 (CCM2883) and NTM R37835 (CCM2885) (males), Tolmer Falls turnoff, Litchfield National Park (13.19654&deg;S; 130.71394&deg;E); NTM R37836 (CCM2936) (female) and WAM R177563 (CCM2937) (female), Florence Falls turnoff, Litchfield National Park (13.12641&deg;S; 130.80463&deg;E).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Diagnosis.&lt;/b&gt; A &lt;i&gt;Gehyra&lt;/i&gt; with moderately small body size (~ 50 mm, range 40&ndash;57 SVL), no flap of skin between limbs, dorsal half of rostral deeply furrowed with groove, single internasal usually present, 2 postnasals usually similar in size but if different then upper larger than lower, first supralabial slightly taller and narrower than second, 2 pairs of chin shields, first digit of manus and pes without claw, moderately flattened snout, snout straight to concave in lateral view, 7 divided subdigital lamellae on fourth toe, in adult males an average of 15 pre-cloacal pores (range 12&ndash;19) arranged in chevron pointing anteriorly. In life, moderately dark tan to brown background colour with pale and dark moderately large spots of similar size and not in contact on dorsum that tend to form transverse rows or coalescing to form short bars.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Description.&lt;/b&gt; Body size moderately small (mean 49.7 mm, range 39.7&ndash;56.7 mm SVL; trunk length moderate (TrunkL/SVL 0.40, 0.36&ndash;0.44), body shape moderately robust and dorsoventrally flattened, moderately flattened head (HD/HL 0.42, 0.38&ndash;0.44) and snout, with short snout (SnEye/HL 0.44, 0.42&ndash;0.46), straight to slightly concave in lateral view, depression between rounded canthal ridges; neck moderately constricted. Limbs moderate length (ArmL/SVL 0.10, 0.08&ndash;0.12; LegL/SVL 0.11, 0.09&ndash;0.13); digits short; claw protruding from dorsal surface of expanded circular to oblong terminal toepad, no claws on anteriormost digit of manus and pes; 7 pairs of subdigitial lamellae on fourth toe (one individual with 6); 1&ndash;3 granular scales between proximate one or two rows of lamellae in 3 of 13 specimens examined.&lt;/p&gt; &lt;p&gt;Nostrils rounded, directed laterally and slightly dorsally, contacted by rostral, supranasal, two postnasals of similar size but upper occasionally larger than lower, and first supralabial; supralabials and infralabials 7&ndash;9; rostral width ~1.7 x height with a deep furrow ~50% of rostral height, a fine medial groove extends 40&ndash;70% of the height of the scale from dorsal edge, surface of rostral with dimpled appearance; supranasals rectangular to round, dorsal edge straight or curved, ventral edge flat and in contact with rostral, supranasals typically separated medially by single small internarial scale (sometimes 2) along dorsal edge of rostral, postnasals of similar size, but upper occasionally larger than lower, first supralabial taller and narrower than second; mental narrow, angling inwards posterior to infralabials, terminating in triangular point, from 1/5 to 1/3 height of inner chin shields; outer chin shields smaller than inner (~1/2 length), with rounded lateral-posterior edges, smaller irregular-sized granular scales lateral to posterior half of outer chin shields; inner chin shields usually in contact or narrowly excluded to second infralabial; first scale of parainfralabial row of scales usually forming a notch on postero-ventral edge of second or third infralabial (if the latter, some granular scales frequently extend to contact second infralabial); chin scale arrangements frequently asymmetric.&lt;/p&gt; &lt;p&gt;Scales on dorsum small, non-overlapping; scales near eyes becoming larger, scales on snout large and rounded; slightly enlarged row of scales above supralabials; scales on ventrum flat and ~6&ndash; 8 x larger than those on dorsum, becoming granular anterior to arms; granular scales on gular region, increasing in size towards parainfralabial row and infralabials; scales on ventral surface of thighs and anterior to cloaca enlarged and flat; medial row of scales on tail greatly enlarged and much wider than long, bordered laterally by 1&ndash;2 rows of moderately enlarged scales, scales on dorsal and lateral surfaces of tail slightly enlarged and tending to be arranged in regular rows; regenerated tails with same scalation, but formed by more irregular scales.&lt;/p&gt; &lt;p&gt;Males (n = 6) with an average of 15 (from 12&ndash;19) pre-cloacal pores forming a shallow chevron with the apex pointed anteriorly, pores penetrating scale, apex pore is generally present; 2 enlarged protruding cloacal spurs to either side of cloaca (females with only slightly enlarged analogous scales). Tail cylindrical and long, tapering to fine point.&lt;/p&gt; &lt;p&gt; &lt;i&gt;Colouration.&lt;/i&gt; In life, background colour of dorsal surfaces dark tan to medium-brown with reddish hues; widely scattered brownish-black dark bars or spots and pale white spots of similar diameter or thickness not in contact and often (but not always) tending to form alternating transverse rows; dark spots usually forming irregularly-shaped bars, but some individuals with roundish spots; midline somewhat lightened in many individuals; dark temporal streak posterior to eye usually present; large dark spots almost extend to eye level on crown but small pale spots or fine stippling extending to snout; supralabials light to heavily stippled with dark pigment, often with maculated appearance formed by hiatus of pigment near sutures; infralabials, mental, chin shields and scales on outer edge of jaw with dark stippling, infralabials often with maculated appearance as for supralabials; upper surfaces of limbs with small pale spots, small dark spots variably expressed, continuing to dorsal surfaces of digits; ventrum pale off-white with light stippling in centre and denser towards lateral edges; dorsal and lateral surfaces of original tails with alternating pale and dark rows of spots; regenerated tails with an admixture of dark and pale scales, some forming longitudinal streaks; ventral surface of tail as for ventrum. In preservative, any reddish hues are lost and background colour is a medium brown.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Habitat.&lt;/b&gt; This species has been collected from sandstone rock formations in open woodland habitats, appearing to prefer large expanses of exposed sandstone such as large boulders and rock walls. It is sympatric with &lt;i&gt;G. nana&lt;/i&gt; and &lt;i&gt;G. koira&lt;/i&gt; (&lt;i&gt;australis&lt;/i&gt; group) at northern localities. The former is a smaller-bodied species that is more commonly found on smaller boulders and amongst rock rubble, whereas &lt;i&gt;G. koira&lt;/i&gt; is much larger and prefers boulders and vertical crevices.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Distribution.&lt;/b&gt; &lt;i&gt;Gehyra paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; occurs in the north-western Northern Territory (Fig. 1). In the east it is abundant in Litchfield National Park, approximately 100 km south of Darwin, south to Butterfly Gorge on the Douglas River. Westernmost records are from the vicinity of Bullo Station near the border of Northern Territory and Western Australia. Recently genotyped specimens from Bradshaw Field Training Area also confirm its presence in the intervening Wingate Range (unpublished data).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology.&lt;/b&gt; The specific name &lt;i&gt;paranana&lt;/i&gt; refers to the morphological similarity of this species to &lt;i&gt;G. nana&lt;/i&gt;, as in &ldquo;parallel to &lt;i&gt;nana&lt;/i&gt; &rdquo;.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Comparisons with other species.&lt;/b&gt; &lt;i&gt;Gehyra paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; resembles &lt;i&gt;G. nana&lt;/i&gt; closely, and the same comparisons to distinguish &lt;i&gt;G. nana&lt;/i&gt; from other &lt;i&gt;Gehyra&lt;/i&gt; above can largely be apply to G. &lt;i&gt;paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; With respect to &lt;i&gt;G. nana&lt;/i&gt;, all but one specimen of &lt;i&gt;G. paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; possessed 7 subdigital lamellae on the fourth toe, whereas &lt;i&gt;G. nana&lt;/i&gt; usually had 5 or 6. For body size, most &lt;i&gt;G. paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; have SVL&gt; 50 mm (maximum SVL is 56.7 mm), whereas most &lt;i&gt;G. nana&lt;/i&gt; have SVL &lt;50 mm; however, some &lt;i&gt;G. nana&lt;/i&gt; from the western Top End (Mt Bundy, Edith Falls, Hayes Creek) do attain larger body size, overlapping the range of &lt;i&gt;G. paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; The pattern of spots is also useful, as &lt;i&gt;G. paranana&lt;/i&gt; &lt;b&gt;sp. nov.&lt;/b&gt; has larger, less distinct, pale spots and dark markings compared to &lt;i&gt;G. nana&lt;/i&gt; (cf. Fig. 5), with the dark markings often forming short bars or networks, especially a dark streak behind the eye (absent in &lt;i&gt;G. nana&lt;/i&gt;).&lt;/p&gt; &lt;p&gt;Owing to the close morphological resemblance of the two species, confirmation of identity is possible with genetics by obtaining a tissue sample (e.g. tail tip) to generate mtDNA SNPs and consulting the diagnostic loci provided in Appendix 2.&lt;/p&gt;Published as part of &lt;i&gt;Doughty, Paul, Bourke, Gayleen, Tedeschi, Leonardo G., Pratt, Renae C., Oliver, Paul M., Palmer, Russell A. &amp; Moritz, Craig, 2018, Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species, pp. 201-244 in Zootaxa 4403 (2)&lt;/i&gt; on pages 215-217, DOI: 10.11646/zootaxa.4403.2.1, &lt;a href="http://zenodo.org/record/1212095"&gt;http://zenodo.org/record/1212095&lt;/a&gt

Macropodid clade support from datasets simulated under coalescence.

<p>(A) Simulation workflow. (B) Mean number of the five nuclear genes supporting each clade in maximum likelihood analyses of 200 simulations of the combined data *BEAST species tree for <i>N</i>_e values of 1,000 (triangle), 10,000 (open circle), 100,000 (square) and 1,000,000 (filled circle). For comparison, the grey bars show the number of genes supporting each clade on the observed data. (C) Percentage of ML analyses supporting each clade among 200 mtDNA simulations on the nuclear-only *BEAST species tree for <i>N</i>_e values set to mitochondrial equivalency for the same populations (one quarter of the corresponding nuclear values). Abbreviations: <i>Lagor</i>.; <i>Lagorchestes</i>, <i>Wall</i>.; <i>Wallabia</i>, <i>M. (Notamac.)</i>; <i>M. (Notamacropus)</i>, <i>M. (Osphran.)</i>; <i>M. (Osphranter)</i>.</p

Phylogenetic relationships of <i>Wallabia</i> and the three <i>Macropus</i> subgenera, <i>M. (Macropus)</i>, <i>M. (Osphranter)</i> and <i>M. (Notamacropus)</i>.

<p>(A) The supertree of Cardillo et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Cardillo1" target="_blank">[6]</a> summarizing previous molecular and morphological phylogenies and (B) Meredith et al.'s <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Meredith1" target="_blank">[7]</a> evolutionary timescale (ave. of four BEAST analyses), showing the 2–2.4 Ma duration divergence cluster. Both trees are modified to include only the taxa sampled in the present study. Dendrolagini was not recovered by Cardillo et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Cardillo1" target="_blank">[6]</a>, however its inclusion in the summary tree is warranted on subsequent strong evidence from morphology <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057745#pone.0057745-Prideaux1" target="_blank">[2]</a> and all recent molecular analyses. Photos include (from the top) <i>W. bicolor</i>, <i>M. rufogriseus</i> (left), <i>M. irma</i> (right), <i>M. rufus and M. giganteus</i>. Photo credits – Matt Phillips, except <i>M. irma</i> (Ric Dawson) and <i>M. rufus</i> (Daniel Hoops).</p

Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species

Doughty, Paul, Bourke, Gayleen, Tedeschi, Leonardo G., Pratt, Renae C., Oliver, Paul M., Palmer, Russell A., Moritz, Craig (2018): Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species. Zootaxa 4403 (2): 201-244, DOI: https://doi.org/10.11646/zootaxa.4403.2.