Non-avian Reptiles Research Articles

More than just the numbers-contrasting response of snake erythrocytes to thermal acclimation.

Acclimation to lower temperatures decreases energy expenditure in ectotherms but increases oxygen consumption in most endotherms, when dropped below thermoneutrality. Such differences should be met by adjustments in oxygen transport through blood. Changes in hematological variables in correspondence to that in metabolic rates are, however, not fully understood, particularly in non-avian reptiles. We investigated the effect of thermal acclimation on a snake model, the grass snakes (Natrix natrix). After 6months of acclimation to either 18°C or 32°C hematocrit, hemoglobin concentration, erythrocyte number, and size were assessed. All variables revealed significantly lower values under warm compared to cold ambient temperature. Our data suggest that non-avian reptiles, similarly as birds, reduce erythrocyte fraction under energy-demanding temperatures. Due to low deformability of nucleated erythrocytes in sauropsids, such reduced fraction may be important in decreasing blood viscosity to optimize blood flow. Novel findings on flexible erythrocyte size provide an important contribution to this optimization process.

Pulmonary Smooth Muscle in Vertebrates: A Comparative Review of Structure and Function.

Although the airways of vertebrates are diverse in shape, complexity, and function, they all contain visceral smooth muscle. The morphology, function, and innervation of this tissue in airways is reviewed in actinopterygians, lungfish, amphibians, non-avian reptiles, birds, and mammals. Smooth muscle was likely involved in tension regulation ancestrally, and may serve to assist lung emptying in fishes and aquatic amphibians, as well as maintain internal lung structure. In certain non-avian reptiles and anurans antagonistic smooth muscle fibers may contribute to intrapulmonary gas mixing. In mammals and birds, smooth muscle regulates airway caliber, and may be important in controlling the distribution of ventilation at rest and exercise, or during thermoregulatory and vocal hyperventilation. Airway smooth muscle is controlled by the autonomic nervous system: cranial cholinergic innervation generally causes excitation, cranial non-adrenergic, non-cholinergic innervation causes inhibition, and spinal adrenergic (SA) input causes species-specific, often heterogeneous contractions and relaxations.

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

Latency in Problem Solving as Evidence for Learning in Varanid and Helodermatid Lizards, with Comments on Foraging Techniques

Cognition and learning have been widely studied in vertebrates, but not across much phylogenetic breadth. Non-avian reptiles, for example, have been poorly studied. Anecdotal observations and a few previous studies suggest that lizards may have strong cognitive skills owing, in part, to behaviors such as optimal foraging and territoriality. We tested four lizard species, including three species of monitor lizard (Varanus spp.) and one species of beaded lizard (Heloderma), in a longitudinal, repeated-trials experimental design using a puzzle-feeder device to evaluate learning, in the form of latency trends over time. We used a Bayesian multilevel modeling statistical method and incorporated unsuccessful trials as censored data. Collectively, all lizards showed a pattern of decreasing latencies over time. We interpret this pattern as learning among our lizards. Notable individual and inter-specific differences were evident, however, suggesting that learning abilities differed among the lizards. In this case, the monitor lizards exhibited steeper declines in latencies and greatly reduced inter-individual variation in comparison to the beaded lizards. Finally, we found differential use of the claws versus the snout among the lizards, which is consistent with a previously posed hypothesis based on different species than we measured.

A systematic review of parasites and micropredators of non-avian reptiles (Reptilia=Sauropsida) in Chile.

Knowledge about the identity of parasites in vertebrates is relevant because of their influence on ecological processes and health of their hosts. This is particularly important for groups of animals currently facing conservation issues, such as reptiles. The diversity of species and supra-specific taxa of microparasites and macroparasites (such as helminths and arthropods) present in non-avian reptiles in Chile was analyzed through a systematic review. A total of 49 scientific documents (thesis projects, abstracts in congresses, book chapters and peer-reviewed articles) concerning parasites, taxonomic descriptions and parasite ecology were included in this review. The suborder Iguania was among the most studied group with 35 native species recognized as hosts of parasites and 39 species of parasites reported up to the category of species or genus. Liolaemus tenuis was the species with the most taxa of recorded parasites (11 taxa, and only three to species level), but Liolaemus chillanensis had the highest number of identified species of parasites. In addition, only one native species of Serpentes, one of Gymnophthalmoidea, and two of Gekkota, as well as some reports of exotic species, were recorded as hosts. Among parasites, Trombidiformes was the richest order with 10 species from the superfamily Pterygosomatoidea and 16 species from Trombiculoidea. Current knowledge about the richness of helminths is very limited and there were only a few records of microparasites. In general, there is an urgent need for the development of collaborative works between specialists in reptile taxonomy and epidemiology in parasitology destined to evaluate the consequences that reptiles and their parasites will suffer due to the ongoing processes of habitat loss, climate change and the still present taxonomic issues of the native reptiles.

Homology, neocortex, and the evolution of developmental mechanisms.

The six-layered neocortex of the mammalian pallium has no clear homolog in birds or non-avian reptiles. Recent research indicates that although these extant amniotes possess a variety of divergent and nonhomologous pallial structures, they share a conserved set of neuronal cell types and circuitries. These findings suggest a principle of brain evolution: that natural selection preferentially preserves the integrity of information-processing pathways, whereas other levels of biological organization, such as the three-dimensional architectures of neuronal assemblies, are less constrained. We review the similarities of pallial neuronal cell types in amniotes, delineate candidate gene regulatory networks for their cellular identities, and propose a model of developmental evolution for the divergence of amniote pallial structures.

Specific MHC class I supertype associated with parasite infection and color morph in a wild lizard population.

The major histocompatibility complex (MHC) is a large gene family that plays a central role in the immune system of all jawed vertebrates. Nonavian reptiles are underrepresented within the MHC literature and little is understood regarding the mechanisms maintaining MHC diversity in this vertebrate group. Here, we examined the relative roles of parasite‐mediated selection and sexual selection in maintaining MHC class I diversity of a color polymorphic lizard. We discovered evidence for parasite‐mediated selection acting via rare‐allele advantage or fluctuating selection as ectoparasite load was significantly lower in the presence of a specific MHC supertype (functional clustering of alleles): supertype four. Based on comparisons between ectoparasite prevalence and load, and assessment of the impact of ectoparasite load on host fitness, we suggest that supertype four confers quantitative resistance to ticks or an intracellular tickborne parasite. We found no evidence for MHC‐associated mating in terms of pair genetic distance, number of alleles, or specific supertypes. An association was uncovered between supertype four and male throat color morph. However, it is unlikely that male throat coloration acts as a signal of MHC genotype to conspecifics because we found no evidence to suggest that male throat coloration predicts male mating status. Overall, our results suggest that parasite‐mediated selection plays a role in maintaining MHC diversity in this population via rare‐allele advantage and/or fluctuating selection. Further work is required to determine whether sexual selection also plays a role in maintaining MHC diversity in agamid lizards.

Stress-Induced Hyperglycemia in White-Throated and White-Crowned Sparrows: A New Technique for Rapid Glucose Measurement in the Field.

Organisms experience stressors, and the physiological response to these stressors is highly conserved. Acute stress activates both the sympathetic nervous system and the hypothalamic-pituitary-adrenal axis, increasing epinephrine, norepinephrine, and glucocorticoids, collectively promoting glucose mobilization. While this is well characterized in mammals, the hyperglycemic response to stress in avian and nonavian reptiles has received less attention. A number of factors, ranging from time of day to blood loss, are reported to influence the extent to which acute stress leads to hyperglycemia in birds. Here we characterized the glycemic response to acute handling stress in two species of free-living sparrows: white-throated sparrows (WTSPs: Zonotrichia albicollis) in St. Mary's County, Maryland, and white-crowned sparrows (WCSPs: Zonotrichia leucophrys) in Tioga Pass Meadow, California. We validated a novel technique for rapid field measurement of glucose using a human blood glucose meter, FreeStyle Lite. As expected, acute handling stress elevated blood glucose at both 15 and 30 min postcapture as compared to baseline for both WTSPs and WCSPs. In addition, handling for 30 min without bleeding had the same hyperglycemic effect as handling with serial bleeds in WCSPs. Finally, body condition that was measured as abdominal fat score predicted stress-induced blood glucose in WTSPs but not in WCSPs. Our results are consistent with the mammalian literature on acute stress and energy mobilization, and we introduce a new field technique for avian field biologists.

A new, three-dimensional geometric morphometric approach to assess egg shape.

This paper proposes a new methodology to quantify patterns of egg shape variation using geometric morphometrics of three-dimensional landmarks captured on digitally reconstructed eggshells and demonstrates its performance in capturing shape variation at multiple biological levels. This methodology offers unique benefits to complement established linear measurement or two-dimensional (2D) contour profiling techniques by (i) providing a more precise representation of eggshell curvature by accounting for variation across the entire surface of the egg; (ii) avoids the occurrence of correlations from combining multiple egg shape features; (iii) avoids error stemming from projecting a highly-curved three-dimensional (3D) object into 2D space; and (iv) enables integration into 3D workflows such as finite elements analysis. To demonstrate, we quantify patterns of egg shape variation and estimate morphological disparity at multiple biological levels, within and between clutches and among species of four passerine species of different lineages, using volumetric dataset obtained from micro computed tomography. The results indicate that species broadly have differently shaped eggs, but with extensive within-species variation so that all four-focal species occupy a range of shapes. Within-species variation is attributed to between-clutch differences in egg shape; within-clutch variation is surprisingly substantial. Recent comparative analyses that aim to explain shape variation among avian taxa have largely ignored potential biases due to within-species variation, or use methods limited to a narrow range of egg shapes. Through our approach, we suggest that there is appreciable variation in egg shape across clutches and that this variation needs to be accounted for in future research. The approach developed in this study to assess variation in shape is freely accessible and can be applied to any spherical-to-conical shaped object, including eggs of non-avian dinosaurs and reptiles through to other extant taxa such as poultry.

Bird-like propagating brain activity in anesthetized Nile crocodiles.

The changes in electroencephalogram (EEG) activity that characterize sleep and its sub-states-slow-wave sleep (SWS) and rapid eye movement (REM) sleep-are similar in mammals and birds. SWS is characterized by EEG slow waves resulting from the synchronous alternation of neuronal membrane potentials between hyperpolarized down-states with neuronal quiescence and depolarized up-states associated with action potentials. By contrast, studies of non-avian reptiles report the presence of high-voltage sharp waves (HShW) during sleep. How HShW relate to EEG phenomena occurring during mammalian and avian sleep is unclear. We investigated the spatiotemporal patterns of electrophysiological phenomena in Nile crocodiles (Crocodylus niloticus) anesthetized with isoflurane to determine whether they share similar spatiotemporal patterns to mammalian and avian slow waves. Recordings of anesthetized crocodiles were made using 64-channel penetrating arrays with electrodes arranged in an 8 × 8 equally spaced grid. The arrays were placed in the dorsal ventricular ridge (DVR), a region implicated in the genesis of HShW. Various aspects of the spatiotemporal distribution of recorded signals were investigated. Recorded signals revealed the presence of HShW resembling those reported in earlier studies of naturally sleeping reptiles. HShW propagated in complex and variable patterns across the DVR. We demonstrate that HShW within the DVR propagate in complex patterns similar to those observed for avian slow waves recorded from homologous brain regions. Consequently, sleep with HShW may represent an ancestral form of SWS, characterized by up-states occurring less often and for a shorter duration than in mammals and birds.

High Temperature, Oxygen, and Performance: Insights from Reptiles and Amphibians.

Much recent theoretical and empirical work has sought to describe the physiological mechanisms underlying thermal tolerance in animals. Leading hypotheses can be broadly divided into two categories that primarily differ in organizational scale: 1) high temperature directly reduces the function of subcellular machinery, such as enzymes and cell membranes, or 2) high temperature disrupts system-level interactions, such as mismatches in the supply and demand of oxygen, prior to having any direct negative effect on the subcellular machinery. Nonetheless, a general framework describing the contexts under which either subcellular component or organ system failure limits organisms at high temperatures remains elusive. With this commentary, we leverage decades of research on the physiology of ectothermic tetrapods (amphibians and non-avian reptiles) to address these hypotheses. Available data suggest both mechanisms are important. Thus, we expand previous work and propose the Hierarchical Mechanisms of Thermal Limitation (HMTL) hypothesis, which explains how subcellular and organ system failures interact to limit performance and set tolerance limits at high temperatures. We further integrate this framework with the thermal performance curve paradigm commonly used to predict the effects of thermal environments on performance and fitness. The HMTL framework appears to successfully explain diverse observations in reptiles and amphibians and makes numerous predictions that remain untested. We hope that this framework spurs further research in diverse taxa and facilitates mechanistic forecasts of biological responses to climate change.

Molecular anatomy of the alligator dorsal telencephalon

The evolutionary relationships of the mammalian neocortex and avian dorsal telencephalon (DT) nuclei have been debated for more than a century. Despite their central importance to this debate, nonavian reptiles remain underexplored with modern molecular techniques. Reptile studies harbor great potential for understanding the changes in DT organization that occurred in the early evolution of amniotes. They may also help clarify the specializations in the avian DT, which comprises a massive, cell-dense dorsal ventricular ridge (DVR) and a nuclear dorsal-most structure, the Wulst. Crocodilians are phylogenetically and anatomically attractive for DT comparative studies: they are the closest living relatives of birds and have a strikingly bird-like DVR, but they also possess a highly differentiated reptile cerebral cortex. We studied the DT of the American alligator, Alligator mississippiensis, at late embryonic stages with a panel of molecular marker genes. Gene expression and cytoarchitectonic analyses identified clear homologs of all major avian DVR subdivisions including a mesopallium, an extensive nidopallium with primary sensory input territories, and an arcopallium. The alligator medial cortex is divided into three components that resemble the mammalian dentate gyrus, CA fields, and subiculum in gene expression and topography. The alligator dorsal cortex contains putative homologs of neocortical input, output, and intratelencephalic projection neurons and, most notably, these are organized into sublayers similar to mammalian neocortical layers. Our findings on the molecular anatomy of the crocodilian DT are summarized in an atlas of the alligator telencephalon.

Incubation temperature influences the behavioral traits of a young precocial bird.

The environment in which animals develop can have important consequences for their phenotype. In reptiles, incubation temperature is a critical aspect of the early developmental environment. Incubation temperature influences morphology, physiology, and behavior of non-avian reptiles, however, little is known about how incubation temperature influences offspring phenotype and behaviors important to avian survival. To investigate whether incubation temperature influences avian behaviors, we collected wood duck (Aix sponsa) eggs from the field and incubated them at three naturally occurring incubation temperatures (35.0, 35.8, and 37.0°C). We conducted multiple repeated behavioral trials on individual ducklings between 5 and 15 days post-hatch to assess activity, exploratory, and boldness behaviors, classified along a proactive-reactive continuum. We measured growth rates and circulating levels of baseline and stress-induced corticosterone levels to investigate possible physiological correlates of behavior. Ducklings incubated at the lowest temperature displayed more proactive behaviors than those incubated at the two higher temperatures. We also found that younger ducklings exhibited more proactive behavior than older ducklings and males exhibited more proactive behavior than females. Further, duckling behaviors were repeatable across time and contexts, indicative of a proactive-reactive continuum of behavioral tendencies. However, neither corticosterone levels nor growth rates were related to behavior. This provides some of the first evidence that incubation temperature, a critical parental effect, influences avian offspring behaviors that may be important for survival. Our results identify incubation temperature as a mechanism that contributes to the development of behavioral traits and, in part, explains how multiple behavioral types may be maintained within populations.

A new lepidosauromorph reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic relationships

ABSTRACTAlthough lepidosaurs are by far the most diverse and widespread group of present-day nonavian reptiles, with over 10,000 formally named species, their early diversification is documented only by a handful of incomplete fossils with few diagnostic features. Recent excavations in strata of the Lower Keuper (Middle Triassic: Ladinian) of Baden-Württemberg, Germany, have yielded abundant skeletal remains of a diversity of small- to medium-sized diapsid reptiles, which include at least three taxa of lepidosauromorphs. One, here named Fraxinisaura rozynekae, is a small-bodied reptile characterized by (1) maxillary and dentary tooth crowns conical, with lingual striae near their apices; (2) maxilla with a dorsoventrally low facial process and long tooth-bearing portion anterior to this process; (3) jugal with a short anterior process and a very short, pointed posterior process; and (4) ilium with a tall, posterodorsally extending blade. Tooth implantation is pleurodont. Size variation in the sample sheds some light on ontogenetic changes, mainly affecting the shape of and ornamentation on cranial bones. Phylogenetic analysis recovered Fraxinisaura rozynekae among Lepidosauromorpha and as the sister taxon of the Middle to Late Jurassic Marmoretta oxoniensis. Unfortunately, currently existing character-taxon matrices do not allow confident resolution of the interrelationships of these and other early Mesozoic lepidosauromorph reptiles.http://zoobank.org/urn:lsid:zoobank.org:pub:02C69A1C-FCC8-4D0C-BA71-79BA30BC9DA7SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Schoch, R. R., and H.-D. Sues. 2018. A new lepidosauromorph reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic relationships. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2018.1444619.

Sex-Chromosome Recombination in Common Frogs Brings Water to the Fountain-of-Youth.

According to the canonical model of sex-chromosome evolution, the degeneration of Y or W chromosomes (as observed in mammals and birds, respectively) results from an arrest of recombination in the heterogametic sex, driven by the fixation of sexually antagonistic mutations. However, sex chromosomes have remained homomorphic in many lineages of fishes, amphibians, and nonavian reptiles. According to the "fountain-of-youth" model, this homomorphy results from occasional events of sex reversal. If recombination arrest in males is controlled by maleness per se (and not by genotype), then Y chromosomes are expected to recombine in XY females, preventing their long-term degeneration. Here, we provide field support for the fountain-of-youth, by showing that sex-chromosome recombination in Rana temporaria only depends on phenotypic sex: naturally occurring XX males show the same restriction of recombination as XY males (average map length ∼2 cM), while XY females recombine as much as XX females (average map length ∼150 cM). Our results challenge several common assumptions regarding the evolution of sex chromosomes, including the role of sexually antagonistic genes as drivers of recombination arrest, and that of chromosomal inversions as underlying mechanisms.

Sex-antagonistic genes, XY recombination and feminized Y chromosomes.

The canonical model of sex-chromosome evolution predicts that sex-antagonistic (SA) genes play an instrumental role in the arrest of XY recombination and ensuing Y chromosome degeneration. Although this model might account for the highly differentiated sex chromosomes of birds and mammals, it does not fit the situation of many lineages of fish, amphibians or nonavian reptiles, where sex chromosomes are maintained homomorphic through occasional XY recombination and/or high turnover rates. Such situations call for alternative explanatory frameworks. A crucial issue at stake is the effect of XY recombination on the dynamics of SA genes and deleterious mutations. Using individual-based simulations, we show that a complete arrest of XY recombination actually benefits females, not males. Male fitness is maximized at different XY recombination rates depending on SA selection, but never at zero XY recombination. This should consistently favour some level of XY recombination, which in turn generates a recombination load at sex-linked SA genes. Hill-Robertson interferences with deleterious mutations also impede the differentiation of sex-linked SA genes, to the point that males may actually fix feminized phenotypes when SA selection and XY recombination are low. We argue that sex chromosomes might not be a good localization for SA genes, and sex conflicts seem better solved through the differential expression of autosomal genes.

Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates.

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.

Molecular and Neuroendocrine Approaches to Understanding Trade-offs: Food, Sex, Aggression, Stress, and Longevity-An Introduction to the Symposium.

SynopsisLife history strategies are composed of multiple fitness components, each of which incurs costs and benefits. Consequently, organisms cannot maximize all fitness components simultaneously. This situation results in a dynamic array of trade-offs in which some fitness traits prevail at the expense of others, often depending on context. The identification of specific constraints and trade-offs has helped elucidate physiological mechanisms that underlie variation in behavioral and physiological life history strategies. There is general recognition that trade-offs are made at the individual and population level, but much remains to be learned concerning the molecular neuroendocrine mechanisms that underlie trade-offs. For example, we still do not know whether the mechanisms that underlie trade-offs at the individual level relate to trade-offs at the population level. To advance our understanding of trade-offs, we organized a group of speakers who study neuroendocrine mechanisms at the interface of traits that are not maximized simultaneously. Speakers were invited to represent research from a wide range of taxa including invertebrates (e.g., worms and insects), fish, nonavian reptiles, birds, and mammals. Three general themes emerged. First, the study of trade-offs requires that we investigate traditional endocrine mechanisms that include hormones, neuropeptides, and their receptors, and in addition, other chemical messengers not traditionally included in endocrinology. The latter group includes growth factors, metabolic intermediates, and molecules of the immune system. Second, the nomenclature and theory of neuroscience that has dominated the study of behavior is being re-evaluated in the face of evidence for the peripheral actions of so-called neuropeptides and neurotransmitters and the behavioral repercussions of these actions. Finally, environmental and ecological contexts continue to be critical in unmasking molecular mechanisms that are hidden when study animals are housed in enclosed spaces, with unlimited food, without competitors or conspecifics, and in constant ambient conditions.

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds.

According to current assemblies, avian genomes differ from those of the other lineages of amniotes in 1) containing a lower number of genes; 2) displaying a high stability of karyotype and recombination map; and 3) lacking any correlation between evolutionary rates (dN/dS) and life-history traits, unlike mammals and nonavian reptiles. We question the reality of the bird missing genes and investigate whether insufficient representation of bird gene content might have biased previous evolutionary analyses. Mining RNAseq data, we show that the vast majority of the genes missing from avian genome assemblies are actually present in most species of birds. These mainly correspond to the GC-rich fraction of the bird genome, which is the most difficult to sequence, assemble and annotate. With the inclusion of these genes in a phylogenomic analysis of high-quality alignments, we uncover a positive and significant correlation between the ratio of nonsynonymous to synonymous substitution rate (dN/dS) and life-history traits in Neoaves. We report a strong effect of GC-biased gene conversion on the dN/dS ratio in birds and a peculiar behavior of Palaeognathae (ostrich and allies) and Galloanserae (chickens, ducks and allies). Avian genomes do not contain fewer genes than mammals or nonavian reptiles. Previous analyses have overlooked ∼15% of the bird gene complement. GC-rich regions, which are the most difficult to access, are a key component of amniote genomes. They experience peculiar molecular processes and must be included for unbiased functional and comparative genomic analyses in birds.

Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles.

As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles.