Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement.

Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould's mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads.

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents.

The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

Red carotenoids and associated gene expression explain colour variation in frillneck lizards.

A long-standing hypothesis in evolutionary ecology is that red-orange ornamental colours reliably signal individual quality owing to limited dietary availability of carotenoids and metabolic costs associated with their production, such as the bioconversion of dietary yellow carotenoids to red ketocarotenoids. However, in ectothermic vertebrates, these colours can also be produced by self-synthesized pteridine pigments. As a consequence, the relative ratio of pigment types and their biochemical and genetic basis have implications for the costs and information content of colour signals; yet they remain poorly known in most taxonomic groups. We tested whether red- and yellow-frilled populations of the frillneck lizard, Chlamydosaurus kingii, differ in the ratio of different biochemical classes of carotenoid and pteridine pigments, and examined associated differences in gene expression. We found that, unlike other squamate reptiles, red hues derive from a higher proportion of ketocarotenoids relative to both dietary yellow carotenoids and to pteridines. Whereas red frill skin showed higher expression of several genes associated with carotenoid metabolism, yellow frill skin showed higher expression of genes associated with steroid hormones. Based on the different mechanisms underlying red and yellow signals, we hypothesize that frill colour conveys different information in the two populations. More generally, the data expand our knowledge of the genetic and biochemical basis of colour signals in vertebrates.

Climate is a strong predictor of near-infrared reflectance but a poor predictor of colour in butterflies.

Colour variation across climatic gradients is a common ecogeographical pattern; yet there is long-standing contention over underlying causes, particularly selection for thermal benefits. We tested the evolutionary association between climate gradients and reflectance of near-infrared (NIR) wavelengths, which influence heat gain but are not visible to animals. We measured ultraviolet (UVA), visible (Vis) and NIR reflectance from calibrated images of 372 butterfly specimens from 60 populations (49 species, five families) spanning the Australian continent. Consistent with selection for thermal benefits, the association between climate and reflectance was stronger for NIR than UVA-Vis wavelengths. Furthermore, climate predicted reflectance of the thorax and basal wing, which are critical to thermoregulation; but it did not predict reflectance of the entire wing, which has a variable role in thermoregulation depending on basking behaviour. These results provide evidence that selection for thermal benefits has shaped the reflectance properties of butterflies.

Revealing the Biochemical and Genetic Basis of Color Variation in a Polymorphic Lizard.

Determining the mechanistic and genetic basis of animal coloration is essential to understand the costs and constraints on color production, and the evolution and maintenance of phenotypic variation. However, genes underlying structural color and widespread pigment classes apart from melanin remain largely uncharacterized, in part due to restricted taxonomic focus. We combined liquid chromatography-mass spectrometry and RNA-seq gene expression analyses to characterize the pigments and genes associated with skin color in the polymorphic lizard, Ctenophorus decresii. Throat coloration in male C. decresii may be a combination of orange, yellow, grey, or ultra-violet blue. We confirmed the presence of two biochemically different pigment classes, pteridines (self-synthesized) and carotenoids (acquired through the diet), in all skin colors. Orange skin had the highest levels of pteridine pigments while yellow skin tended to have higher levels of carotenoids, of which the vitamin A precursors ß-carotene and ß-cryptoxanthin have not been previously confirmed in reptiles. These results were confirmed by gene expression analyses, which detected 489 genes differentially expressed between the skin colors, including genes associated with pteridine production, provitamin A carotenoid metabolism, iridophore-specific synthesis, melanin synthesis, and steroid hormone pathways. For the majority of these 489 genes, however, our study reveals a new association with color production in vertebrates. These data represent a significant contribution to understanding the genetic basis of color variation in vertebrates and a rich resource for further studies.

An Exon-Capture System for the Entire Class Ophiuroidea.

Exon-capture studies have typically been restricted to relatively shallow phylogenetic scales due primarily to hybridization constraints. Here, we present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures approximately 90% of the 1,552 exon target, across all major lineages of the quarter-billion-year-old extant crown group. Key features of our system are 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map, or align; 2) use of multiple artificial representatives based on ancestral state reconstructions rather than exemplars to improve capture and mapping of the target; 3) mapping reads to a multi-reference alignment; and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences, and sample contamination. The resulting data give a well-resolved tree (currently standing at 417 samples, 275,352 sites, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.

Deep molecular divergence and exceptional morphological stasis in dwarf cannibal snails Nata sensu lato Watson, 1934 (Rhytididae) of southern Africa.

The genus Nata Watson, 1934 is a southern African endemic belonging to the Gondwanan family of carnivorous snails, Rhytididae. We present a molecular phylogeny of the genus based on two mitochondrial (16S and COI) and two nuclear genes (ITS2 and 28S RNA), and complement this with an appraisal of morphological characters relating to both the shell and soft parts. We identify four reciprocally monophyletic lineages for which valid names are already available, plus two undescribed species restricted to the Albany Thicket Biome. We show that Nata sensu lato may not be monophyletic. Rather there exist two deep lineages within Nata s.l., one lineage potentially sister to a clade dominated by the Australian and New Zealand radiation, and the other occupying a basal position within Rhytididae. Accordingly we recommend a revision recognising two genera, namely Nata s.s. and Natella respectively. Despite deep molecular divergences within Nata s.s., phenotypic evolution has been remarkably conserved, and contrasts greatly with that exhibited across other major lineages within the Rhytididae.

Environment, but not genetic divergence, influences geographic variation in colour morph frequencies in a lizard.

BACKGROUND: Identifying the causes of intraspecific phenotypic variation is essential for understanding evolutionary processes that maintain diversity and promote speciation. In polymorphic species, the relative frequencies of discrete morphs often vary geographically; yet the drivers of spatial variation in morph frequencies are seldom known. Here, we test the relative importance of gene flow and natural selection to identify the causes of geographic variation in colour morph frequencies in the Australian tawny dragon lizard, Ctenophorus decresii. RESULTS: Populations of C. decresii are polymorphic for male throat coloration and all populations surveyed shared the same four morphs but differed in the relative frequencies of morphs. Despite genetic structure among populations, there was no relationship between genetic similarity or geographic proximity and similarity in morph frequencies. However, we detected remarkably strong associations between morph frequencies and two environmental variables (mean annual aridity index and vegetation cover), which together explained approximately 45 % of the total variance in morph frequencies. CONCLUSIONS: Spatial variation in selection appears to play an important role in shaping morph frequency patterns in C. decresii. Selection associated with differences in local environmental conditions, combined with relatively low levels of gene flow, is expected to favour population divergence in morph composition, but may be counteracted by negative frequency-dependent selection favouring rare morphs.

Spectral sensitivity of cone photoreceptors and opsin expression in two colour-divergent lineages of the lizard Ctenophorus decresii.

Intraspecific differences in sensory perception are rarely reported but may occur when a species range extends across varying sensory environments, or there is coevolution between the sensory system and a varying signal. Examples in colour vision and colour signals are rare in terrestrial systems. The tawny dragon lizard Ctenophorus decresii is a promising candidate for such intraspecific variation, because the species comprises two geographically and genetically distinct lineages in which throat colour (a social signal used in intra- and inter-specific interactions) is locally adapted to the habitat and differs between lineages. Male lizards from the southern lineage have UV-blue throats, whereas males from the northern lineage are polymorphic with four discrete throat colours that all show minimal UV reflectance. Here, we determine the cone photoreceptor spectral sensitivities and opsin expression of the two lineages, to test whether they differ, particularly in the UV wavelengths. Using microspectrophotometry on retinal cone photoreceptors, we identified a long-wavelength-sensitive (LWS) visual pigment, a 'short' and 'long' medium-wavelength-sensitive (MWS) pigment and a short-wavelength-sensitive (SWS) pigment, all of which did not differ in λmax between lineages. Through transcriptome analysis of opsin genes we found that both lineages express four cone opsin genes, including the SWS1 opsin with peak sensitivity in the UV range, and that amino acid sequences did not differ between lineages with the exception of a single leucine to valine substitution in the RH2 opsin. Counts of yellow and transparent oil droplets associated with LWS+MWS and SWS+UVS cones, respectively, showed no difference in relative cone proportions between lineages. Therefore, contrary to predictions, we find no evidence of differences between lineages in single cone photoreceptor spectral sensitivity or opsin expression. However, we confirm the presence of four single cone classes, suggesting tetrachromacy in C. decresii, and we also provide the first evidence of UV sensitivity in agamid lizards.

Phylogenetic evidence of historic mitochondrial introgression and cryptic diversity in the genus Pseudemoia (Squamata: Scincidae).

The Australian scincid genus Pseudemoia comprises six morphologically similar species restricted to temperate south-eastern Australia. Due to the high degree of morphological conservatism, phylogenetic relationships and taxonomic status within the Pseudemoia entrecasteauxii complex (comprising the nominal species P. entrecasteauxii, P. cryodroma, and P. pagenstecheri) remains unresolved. To further investigate the phylogenetic relationships and taxonomic status of Pseudemoia spp., and to test the hypothesis that P. cryodroma evolved from hybridization between P. entrecasteauxii and P. pagenstecheri, we sequenced one mitochondrial locus (ND4) and five nuclear loci (ß-globin, LGMN, PRLR, Rhodopsin, RPS8). While we find strong support for the monophyly of the P. entrecasteauxii complex, there exists marked incongruence between the mitochondrial and nuclear markers, particularly in regards to the high altitude specialist, P. cryodroma. The most parsimonious explanation of this discordance is historic mitochondrial introgression, although a hybrid origin for P. cryodroma cannot be completely rejected. Within P. pagenstecheri sensu lato, we identified a strongly supported, highly divergent yet morphologically cryptic lineage restricted to northern New South Wales. Although more weakly supported by the nuDNA, we also identified a second geographically distinct lineage of P. pagenstecheri s.l., which may warrant separate conservation management. Our study reveals a more complex evolutionary history of the genus Pseudemoia than previously appreciated and contributes to our understanding of the biogeography and evolution of Australian mesic zone fauna.

Genetic diversity of a short-ranged endemic terrestrial snail.

The factors that influence population structure and connectivity are unknown for most terrestrial invertebrates but are of particular interest both for understanding the impacts of disturbance and for determining accurate levels of biodiversity and local endemism. The main objective of this study was to determine the historical patterns of genetic differentiation and contemporary gene flow in the terrestrial snail, Austrochloritis kosciuszkoensis (Shea & O. L. Griffiths, 2010). Snails were collected in the Mt Buffalo and Alpine National Parks in Victoria, in a bid to understand how populations of this species are connected both within continuous habitat and between adjacent, yet separate environments. Utilising both mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, the degree of population structure was determined within and between sites. Very high levels of genetic divergence were found between the Mt Buffalo and Alpine snails, with no evidence for genetic exchange detected between the two regions, indicating speciation has possibly occurred between the two regions. Our analyses of the combined mtDNA and nDNA (generated from SNPs) data have revealed patterns of genetic diversity that are consistent with a history of long-term isolation and limited connectivity. This history may be related to past cycles of changes to the climate over hundreds of thousands of years, which have, in part, caused the fragmentation of Australian forests. Within both regions, extremely limited gene flow between separate populations suggests that these land snails have very limited dispersal capabilities across existing landscape barriers, especially at Mt Buffalo: here, populations only 5 km apart from each other are genetically differentiated. The distinct genetic divergences and clearly reduced dispersal ability detected in this data explain the likely existence of at least two previously unnamed cryptic Austrochloritis species within a 30-50 km radius, and highlight the need for more concentrated efforts to understand population structure and gene flow in terrestrial invertebrates.

New Guinea uplift opens ecological opportunity across a continent.

Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.

Selection for social signalling drives the evolution of chameleon colour change.

Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages. The two principal explanations for the evolution of this adaptive strategy are (1) natural selection for crypsis (camouflage) against a range of different backgrounds and (2) selection for conspicuous social signals that maximise detectability to conspecifics, yet minimise exposure to predators because they are only briefly displayed. Here we show that evolutionary shifts in capacity for colour change in southern African dwarf chameleons (Bradypodion spp.) are associated with increasingly conspicuous signals used in male contests and courtship. To the chameleon visual system, species showing the most dramatic colour change display social signals that contrast most against the environmental background and amongst adjacent body regions. We found no evidence for the crypsis hypothesis, a finding reinforced by visual models of how both chameleons and their avian predators perceive chameleon colour variation. Instead, our results suggest that selection for conspicuous social signals drives the evolution of colour change in this system, supporting the view that transitory display traits should be under strong selection for signal detectability.

Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents.

Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e., carnivores and herbivores) than in ancestral forms (i.e., omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents.

Variable responses of skinks to a common history of rainforest fluctuation: concordance between phylogeography and palaeo-distribution models.

There is a growing appreciation of impacts of late-Quaternary climate fluctuations on spatial patterns of species and genetic diversity. A major challenge is to understand how and why species respond individualistically to a common history of climate-induced habitat fluctuation. Here, we combine modelling of palaeo-distributions and mitochondrial-DNA phylogeographies to compare spatial patterns of population persistence and isolation across three species of rainforest skinks (Saproscincus spp.) with varying climatic preferences. Using Akaike Information Criterion model-averaged projections, all three species are predicted to have maintained one or more small populations in the northern Wet Tropics, multiple or larger populations in the central region, and few if any in the south. For the high-elevation species, Saproscincus czechurai, the warm-wet climate of the mid Holocene was most restrictive, whereas for the generalist S. basiliscus and lower-elevation S. tetradactyla, the cool-dry last glacial maximum was most restrictive. As expected, S. czechurai was the most genetically structured species, although relative to modelled distributions, S. basiliscus had surprisingly deep phylogeographical structure among southern rainforest isolates, implying long-term isolation and persistence. For both S. basiliscus and S. tetradactyla, there was high genetic diversity and complex phylogeographical patterns in the central Wet Tropics, reflecting persistence of large, structured populations. A previously identified vicariant barrier separating northern and central regions is supported, and results from these species also emphasize a historical persistence of populations south of another biogeographical break, the Tully Gorge. Overall, the results support the contention that in a topographically heterogeneous landscape, species with broader climatic niches may maintain higher and more structured genetic diversity due to persistence through varying climates.

A phylogeny of the cannibal snails of southern Africa, genus Natalina sensu lato (Pulmonata: Rhytididae): assessing concordance between morphology and molecular data.

The genus Natalina Pilsbry, 1893 is a southern African endemic belonging to the Gondwanan family of carnivorous snails, Rhytididae. We present a well-resolved molecular phylogeny of the genus based on the mitochondrial 16S and COI genes and the nuclear ITS2 gene, and assess this in light of Watson's [Watson, H., 1934. Natalina and other South African snails. Proc. Malacol. Soc. Lond. 21, 150-193] supra-specific classification via a re-examination of 23 morphological characters including features of the shell, radula, external anatomy and distal reproductive tract. Ancestral reconstruction and character mapping based on the MK(1) model reveals broad concordance between morphology and the molecular phylogeny at the supra-specific level. Given this concordance and exceptionally deep divergences in the molecular data, we recommend the elevation of the subgenera Natalina s.s., Afrorhytida, and Capitina to generic status. At the species level, we identify several species complexes for which additional fine scale morphological and molecular appraisal is needed to qualify on the one hand incipient speciation with notable differentiation in shell form and body pigmentation, and on the other, phylogenetically deep yet morphologically cryptic diversity.

Conserved visual sensitivities across divergent lizard lineages that differ in an ultraviolet sexual signal.

The sensory drive hypothesis predicts the correlated evolution of signaling traits and sensory perception in differing environments. For visual signals, adaptive divergence in both color signals and visual sensitivities between populations may contribute to reproductive isolation and promote speciation, but this has rarely been tested or shown in terrestrial species. We tested whether opsin protein expression differs between divergent lineages of the tawny dragon (Ctenophorus decresii) that differ in the presence/absence of an ultraviolet sexual signal. We measured the expression of four retinal cone opsin genes (SWS1, SWS2, RH2, and LWS) using droplet digital PCR. We show that gene expression between lineages does not differ significantly, including the UV wavelength sensitive SWS1. We discuss these results in the context of mounting evidence that visual sensitivities are highly conserved in terrestrial systems. Multiple competing requirements may constrain divergence of visual sensitivities in response to sexual signals. Instead, signal contrast could be increased via alternative mechanisms, such as background selection. Our results contribute to a growing understanding of the roles of visual ecology, phylogeny, and behavior on visual system evolution in reptiles.

Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard.

Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region.