Tetrapod Vertebrates Research Articles

Birds Generally Carry a Small Repertoire of Bitter Taste Receptor Genes.

As they belong to the most species-rich class of tetrapod vertebrates, birds have long been believed to possess an inferior taste system. However, the bitter taste is fundamental in birds to recognize dietary toxins (which are typically bitter) in potential food sources. To characterize the evolution of avian bitter taste receptor genes (Tas2rs) and to test whether dietary toxins have shaped the repertoire size of avian Tas2rs, we examined 48 genomes representing all but 3 avian orders. The total number of Tas2r genes was found to range from 1 in the domestic pigeon to 12 in the bar-tailed trogon, with an average of 4, which suggested that a much smaller Tas2r gene repertoire exists in birds than in other vertebrates. Furthermore, we uncovered a positive correlation between the number of putatively functional Tas2rs and the abundance of potential toxins in avian diets. Because plant products contain more toxins than animal tissues and insects release poisonous defensive secretions, we hypothesized that herbivorous and insectivorous birds may demand more functional Tas2rs than carnivorous birds feeding on noninsect animals. Our analyses appear to support this hypothesis and highlight the critical role of taste perception in birds.

Digit ratios in two lacertid lizards: sexual dimorphism and morphological and physiological correlates

Digit length ratio (primarily 2D:4D) has become increasingly popular as a possible biomarker of intrauterine steroid exposure in the human medical, social and psychological literature. Human males tend to have lower digit ratios than females, and individuals with low ratios tend to excel in physical performance, especially in endurance-related sports. Because early limb development is evolutionarily conservative, it has been speculated that these trends should also be visible in other tetrapod vertebrates. However, studies on non-human vertebrates are scant, and their results suggest that sexual dimorphism in digit ratios and the associations with physical performance are much more intricate and taxon-specific than presumed. In this study, we compared digit ratios of two Podarcis lizards among sexes, colour morphs and species. We also tested for associations with three performance characteristics that are of ecological relevance. Both species examined exhibit male-larger sexual dimorphism in digit ratio. 2D:4D, 3D:4D and 2D:3D ratios are tightly correlated within the manus and the pes, but less so between manus and pes. In the colour polymorphic species P. melisellensis, the yellow morph exhibits higher dimorphism than the orange and white morphs. Digit ratios did not correlate with individual performance for sprint speed or endurance, but within males of P. melisellensis, individuals with higher digit ratios correlated positively with head size and bite force. We conclude that digit ratios in lizards deserve attention, because they exhibit sexual dimorphism and correlate with ecologically relevant morphological and performance variables. As lizard species differ widely in mating systems, reproductive mode, habitat use and locomotor behaviour, they seem excellent model animals for studying patterns in digit length ratios.

Substrate Diameter and Orientation in the Context of Food Type in the Gray Mouse Lemur, Microcebus murinus: Implications for the Origins of Grasping in Primates

Grasping is a widespread behavior among tetrapod vertebrates. In primates, the hands and feet are involved in many tasks including arboreal locomotion and food acquisition. Yet, the origin and the evolution of prehensile capacities, which are highly diversified across this group, remain open for inquiry. Some researchers suggest that grasping evolved in an arboreal habitat consisting of fine branches associated with insect predation and/or fruit and flower exploitation. However, few studies have tested the importance of arboreal conditions and diet, e.g., frugivorous, omnivorous, on the use of the hands in food grasping. The aim of this study was to link substrate use and food grasping strategies quantitatively to test hypotheses concerning primate grasping origins. We studied a species often described as a good ecological model to study the origin of grasping in primates, Microcebus murinus, and quantified its spontaneous substrate use (diameter and orientation) in an unconstrained environment while presenting them with different food types (static and mobile). We show that 1) Microcebus murinus appears to be an opportunistic rather than a specialist user of fine branches as suggested previously, at least under laboratory conditions; and 2) food properties had an impact on the use of the hands vs. the mouth, with the hands being used more for the grasping of mobile prey. Our results are consistent with hypotheses for primate origins that propose adaptations to both a narrow branch environment and visually directed prey capture with the hands. However, additional studies in the wild are needed to understand better the origin and increased use of the hands in primates grasping and manipulation.

TALEN-mediated apc mutation in Xenopus tropicalis phenocopies familial adenomatous polyposis.

Truncating mutations in the tumor suppressor gene adenomatous polyposis coli (APC) are the initiating step in the vast majority of sporadic colorectal cancers, and they underlie familial adenomatous polyposis (FAP) syndromes. Modeling of APC- driven tumor formation in the mouse has contributed substantially to our mechanistic understanding of the associated disease, but additional models are needed to explore therapeutic opportunities and overcome current limitations of mouse models. We report on a novel and penetrant genetic cancer model in Xenopus tropicalis, an aquatic tetrapod vertebrate with external development, diploid genome and short life cycle. Tadpoles and froglets derived from embryos injected with TAL effector nucleases targeting the apc gene rapidly developed intestinal hyperplasia and other neoplasms observed in FAP patients, including desmoid tumors and medulloblastomas. Bi-allelic apc mutations causing frame shifts were detected in the tumors, which displayed activation of the Wnt/β-catenin pathway and showed increased cellular proliferation. We further demonstrate that simultaneous double bi-allelic mutation of apc and a non-relevant gene is possible in the neoplasias, opening the door for identification and characterization of effector or modifier genes in tumors expressing truncated apc. Our results demonstrate the power of modeling human cancer in Xenopus tropicalis using mosaic TALEN-mediated bi-allelic gene disruption.

Development of the nasolacrimal apparatus in the Mongolian gerbil (Meriones unguiculatus), with notes on network topology and function.

The nasolacrimal apparatus (NLA) is a multicomponent functional system comprised of multiple orbital glands (up to four larger multicellular exocrine structures), a nasal chemosensory structure (vomeronasal organ: VNO), and a connecting duct (nasolacrimal duct: NLD). Although this system has been described in all tetrapod vertebrate lineages, albeit not always with all three main components present, considerably less is known about its ontogeny. The Mongolian gerbil (Meriones unguiculatus) is a common lab rodent in which the individual components of the adult NLA have been well studied, but as yet nothing is known about the ontogeny of the NLA. In this study, serial sections of 15 fetal and three adult Mongolian gerbil heads show that the development of the NLA falls into three fetal stages: inception (origin of all features), elongation (lengthening of all features), and expansion (widening of all features). No postnatal or juvenile specimens were observed in this study, but considerable growth evidently occurs before the final adult condition is reached. The development of the orbital glands and the VNO in the Mongolian gerbil is largely consistent with those in other mammals, despite a slight nomenclatural conundrum for the anterior orbital glands. However, the Mongolian gerbil NLD follows a more circuitous route than in other tetrapods, due mainly to the convoluted arrangement of the narial cartilages, the development of a pair of enlarged incisors as well as an enlarged infraorbital foramen. The impact of these associated features on the ontogeny and phylogeny of the NLA could be examined through the approach of network science. This approach allows for the incorporation of adaptations to specific lifestyles as potential explanations for the variation observed in the NLA across different tetrapod clades.

Reevaluation of the homology of bones of the cranial vault in tetrapod vertebrates

Homology assessments of bones are made using one or more criteria (e.g., topology, development, phylogeny). In tetrapods, the bones of the cranial vault appear highly conserved topologically. However, recent fate maps have revealed key differences in the embryonic origin of bones of the cranial vault in representatives of two amniote lineages. In mouse, the frontal is derived from cranial neural crest (CNC) and the parietal of mesoderm, placing the CNC-mesoderm boundary at the suture between these bones. In chicken, by contrast, this boundary is located within the frontal, which thus has a dual embryonic origin. This difference is seemingly inconsistent with the traditional assessment of homology of the avian frontal with that of mammals and other tetrapods. To elucidate this apparent conflict, we fate-mapped CNC and mesoderm using GFP-transgenic axolotls to reveal specific contributions to the cranial vault. The CNC-mesoderm boundary in axolotl is located between frontal and parietal, as in mouse, but differs from that in chicken. If, however, the avian frontal is instead regarded as a fused frontal and parietal (i.e., frontoparietal) and the parietal a postparietal, then the avian cranial vault remains topologically congruent, and becomes developmentally congruent, with that of both urodeles and mammals. This hypothesis is supported by data from the fossil record: a separate frontal, parietal and postparietal is present in all stem lineages of extant taxa, including birds. Moreover, it implies that a postparietal is/was present in non-avian archosaurs but likely fuses early in ontogeny to the parietal (or supraoccipital), as it does in many extant mammals.

Conhecimentos e usos da fauna por caçadores no semiárido brasileiro: um estudo de caso no estado da Paraíba, Nordeste do Brasil

The present study was undertaken in a traditional community in the semiarid region of Paraiba State, Northeastern Brazil, with the purpose of registering the main animal species hunted and evaluating the implications of these practices in terms of the conservation of local fauna. A total of 78 species of wild tetrapod vertebrates were cited by 24 interviewees as being hunted in the region. These animals were separated into four different animals groups (mammals, birds, reptiles and amphibians) with ten distinct purposes: zootherapy, folk veterinary medicine, cosmetics, mystical-religious purposes, creation/domestication, commercial exploration, ornamental use, as food, as entertainment, and for animal control. This work highlights the lack of studies regarding some forms of exploitation of wildlife resources as a barrier that hinders the assessment of priorities for conservation and management, by precluding a stable inventory of animal species under the greatest pressure of use. However, even with these barriers we can clearly see that exploitation and utilization of wildlife by man represents one of the most significant uses of natural resources in the surveyed areas.

Homoiterons and expansion in ribosomal RNAs

Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron-rich double-stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Regulation of tyrosine hydroxylase transcription by hnRNP K and DNA secondary structure.

Regulation of tyrosine hydroxylase gene (Th) transcription is critical for specifying and maintaining the dopaminergic neuronal phenotype. Here we define a molecular regulatory mechanism for Th transcription conserved in tetrapod vertebrates. We show that heterogeneous nuclear ribonucleoprotein (hnRNP) K is a transactivator of Th transcription. It binds to previously unreported and evolutionarily conserved G:C-rich regions in the Th proximal promoter. hnRNP K directly binds C-rich single DNA strands within these conserved regions and also associates with double-stranded sequences when proteins, such as CREB, are bound to an adjacent cis-regulatory element. The single DNA strands within the conserved G:C-rich regions adopt either G-quadruplex or i-motif secondary structures. We also show that small molecule-mediated stabilization of these secondary structures represses Th promoter activity. These data suggest that these secondary structures are targets for pharmacological modulation of the dopaminergic phenotype.

K-Pg events facilitated lineage transitions between terrestrial and aquatic ecosystems.

We use dated phylogenetic trees for tetrapod vertebrates to identify lineages that shifted between terrestrial and aquatic ecosystems in terms of feeding or development, and to assess the timing of such events. Both stem and crown lineage ages indicate a peak in transition events in correspondence with the K-Pg mass extinction. This meets the prediction that changes in competitive pressure and resource availability following mass extinction events should facilitate such transitions.

Mechanisms underlying vertebrate limb regeneration: lessons from the salamander.

Limb regeneration in adult salamanders proceeds by formation of a mound of progenitor cells called the limb blastema. It provides several pointers for regenerative medicine. These include the role of differentiated cells in the origin of the blastema, the role of regenerating axons of peripheral nerves and the importance of cell specification in conferring morphogenetic autonomy on the blastema. One aspect of regeneration that has received less attention is the ability to undergo multiple episodes without detectable change in the outcome, and with minimal effect of aging. We suggest that, although such pointers are valuable, it is important to understand why salamanders are the only adult tetrapod vertebrates able to regenerate their limbs. Although this remains a controversial issue, the existence of salamander-specific genes that play a significant role in the mechanism of regeneration provides evidence for the importance of local evolution, rather than a purely ancestral mechanism. The three-finger protein called Prod1 is discussed in the present article as an exemplar of this approach.

Chapter 8 - Expiration: Breathing's other face

The evolution of the aspiration pump seen in tetrapod vertebrates from the buccal-pharyngeal force pump seen in air breathing fish and amphibians appears to have first involved the production of active expiration. Active inspiration arose later. This appears to have involved reconfiguration of a parafacial oscillator (now the parafacial respiratory group/retrotrapezoid nucleus (pFRG/RTN)) to produce active expiration, followed by reconfiguration of a paravagal oscillator (now the preBötC) to produce active inspiration. In the ancestral breathing cycle, inspiration follows expiration, which is in turn followed by glottal closure and breath holding. When both rhythms are expressed, as they are in reptiles and birds, and mammals under conditions of elevated respiratory drive, the pFRG/RTN appears to initiate the respiratory cycle. We propose that the coordinated output of this system is a ventilation cycle characterized by four phases. In reptiles, these consist of active inspiration (I), glottal closure (E1), a pause (an apnea or breath hold) (E2), and an active expiration (E3) that initiates the next cycle. In mammals under resting conditions, active expiration (E3) is suppressed and inspiration (I) is followed by airway constriction and diaphragmatic braking (E1) (rather than glottal closure) and a short pause at end-expiration (E2). As respiratory drive increases in mammals, expiratory muscle activity appears. Frequently, it first appears immediately preceding inspiration (E3) just as it does in reptiles. It can also appear in E1, however, and it is not yet clear what mechanisms underlie when and where in the cycle it appears. This may reflect whether the active expiration is recruited to enhance tidal volume, increase breathing frequency, or both.

Attenuation of bone morphogenetic protein signaling during amphibian limb development results in the generation of stage‐specific defects

The vertebrate limb is one of the most intensively studied organs in the field of developmental biology. Limb development in tetrapod vertebrates is highly conserved and dependent on the interaction of several important molecular pathways. The bone morphogenetic protein (BMP) signaling cascade is one of these pathways and has been shown to be crucial for several aspects of limb development. Here, we have used a Xenopus laevis transgenic line, in which expression of the inhibitor Noggin is under the control of the heat-shock promoter hsp70 to examine the effects of attenuation of BMP signaling at different stages of limb development. Remarkably different phenotypes were produced at different stages, illustrating the varied roles of BMP in development of the limb. Very early limb buds appeared to be refractory to the effects of BMP attenuation, developing normally in most cases. Ectopic limbs were produced by overexpression of Noggin corresponding to a brief window of limb development at about stage 49/50, as recently described by Christen etal. (2012). Attenuation of BMP signaling in stage 51 or 52 tadpoles lead to a reduction in the number of digits formed, resulting in hypodactyly or ectrodactyly, as well as occasional defects in the more proximal tibia-fibula. Finally, inhibition at stage 54 (paddle stage) led to the formation of dramatically shortened digits resulting from loss of distal phalanges. Transcriptome analysis has revealed the possibility that more Noggin-sensitive members of the BMP family could be involved in limb development than previously suspected. Our analysis demonstrates the usefulness of heat-shock-driven gene expression as an effective method for inhibiting a developmental pathway at different times during limb development.

Eighty‐three lineages that took over the world: a first review of terrestrial cosmopolitan tetrapods

AbstractAimWhile there is a huge macroecological and biogeographical literature addressing endemism, very little has been done to systematically study lineages that are widely distributed across the globe. Our aim here was to list and analyse those lineages of terrestrial tetrapod vertebrates found in 60–90% of the world, loosely termed here as cosmopolitan.LocationGlobal.MethodsTwo sets of geographical units and three occupancy criteria were used to list, analyse and map cosmopolitan lineages and their sister lineages.ResultsAmong the 83 lineages identified, 2 were represented by amphibians, 9 by reptiles, 13 by mammals, and the remainder by birds, of which 12 were passerines and 47 were non‐passerines. All these lineages are present in parts of Southeast Asia, most of them throughout much of Eurasia and Africa, but fewer in South America and very few in Australia. Only three of the lineages (all reptiles) are likely to exemplify vicariance or early dispersal‐driven cosmopolitanism, the rest having attained world‐wide distribution via extensive, geologically recent dispersal. The distribution of sister lineages indicates that many cosmopolitan lineages probably originated in the savanna regions of Africa, some in Southeast Asia, and fewer in tropical America.Main conclusionsCosmopolitan distributions in tetrapods are primarily the result of dispersal, with large body size and the ability to fly being two key correlates of rapid global colonization. We argue that a cosmopolitan lineage framework in biogeographical and ecological studies could add great depth to the understanding of evolutionary success, and would be highly relevant to the field of invasion biology.

EXCRETORY NITROGEN METABOLISM AND GLUCONEOGENESIS DURING DEVELOPMENT OF HIGHER VERTEBRATES

ABSTRACT The concept of nitrogen “excretion” by mammalian and avian embryos is examined in light of contemporary knowledge of hepatic metabolism. The origin of “waste” nitrogen and the hepatic pathways for its conversion to either urea or uric acid for excretion are described. The probable evolution of these pathways among the higher tetrapod vertebrates and the impact of the selective advantage of uricoteley on the radiation of the archosaurs are considered. The intimate connection of hepatic gluconeogenesis with nitrogenous end product formation in birds and mammals is examined. Finally, the development of the capacities for gluconeogenesis and for either ureogenesis or urieogenesis in the perinate is discussed relative to the problem of development in a cleidoic egg.

Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hoxstructure for non-mammalian tetrapod vertebrates?

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13–hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates.

Vocal‐motor and auditory connectivity of the midbrain periaqueductal gray in a teleost fish

The midbrain periaqueductal gray (PAG) plays a central role in the descending control of vocalization across vertebrates. The PAG has also been implicated in auditory-vocal integration, although its precise role in such integration remains largely unexplored. Courtship and territorial interactions in plainfin midshipman fish depend on vocal communication, and the PAG is a central component of the midshipman vocal-motor system. We made focal neurobiotin injections into the midshipman PAG to both map its auditory-vocal circuitry and allow evolutionary comparisons with tetrapod vertebrates. These injections revealed an extensive bidirectional pattern of connectivity between the PAG and known sites in both the descending vocal-motor and the ascending auditory systems, including portions of the telencephalon, dorsal thalamus, hypothalamus, posterior tuberculum, midbrain, and hindbrain. Injections in the medial PAG produced dense label within hindbrain auditory nuclei, whereas those confined to the lateral PAG preferentially labeled hypothalamic and midbrain auditory areas. Thus, the teleost PAG may have functional subdivisions playing different roles in vocal-auditory integration. Together the results confirm several pathways previously identified by injections into known auditory or vocal areas and provide strong support for the hypothesis that the teleost PAG is centrally involved in auditory-vocal integration.

Vertebrate extracellular calcium-sensing receptor evolution: Selection in relation to life history and habitat

Ionic calcium (Ca2+) supports essential functions within physiological systems, and consequently its concentration is homeostatically regulated within narrow bounds in the body fluids of animals through endocrine effects at ion-transporting osmoregulatory tissues. In vertebrates, extracellular Ca2+ is detected at the cell surface by the extracellular calcium-sensing receptor (CaSR), a member of the G protein-coupled receptor (GPCR) superfamily. Interestingly, the taxonomic distribution of CaSRs is restricted to vertebrates, with some CaSR-like receptors apparently present in non-vertebrate chordates. Since bone is a known Ca2+ storage site and is characteristically restricted to the vertebrate lineage, we hypothesized a functional association of CaSR with vertebrate skeleton that may have an ancient origin. Protein sequence alignment and phylogenetic analysis of vertebrate CaSRs and related GPCRs of the glutamate receptor-like family expose similarities and indel differences among these receptors, and reveal the evolutionary history of CaSRs. Evolutionary selection was tested statistically by evaluating the relationship between non-synonymous (replacement, dN) versus synonymous (silent, dS) amino acid substitution rates (as dN/dS) of protein-coding DNA sequences among branches of the estimated protein phylogeny. On a background of strong purifying selection (dN/dS<1) in the CaSR phylogeny, statistical evidence for adaptive evolution (dN/dS>1) was detected on some branches to major clades in the CaSR phylogeny, especially to the tetrapod vertebrate CaSRs and chordate CaSR-like branches. Testing also revealed overall purifying selection at the codon level. At some sites relaxation from strong purifying selection was seen, but evidence for adaptive evolution was not detected for individual sites. The results suggest purifying selection of CaSRs, and of adaptive evolution among some major vertebrate clades, reflecting clade specific differences in natural history and organismal biology, including skeletal involvement in calcium homeostasis.

A rapid multi-disciplinary biodiversity assessment of the Kamdebooberge (Sneeuberg, Eastern Cape, South Africa): implications for conservation

Botanical work since 2008 on the Sleeping Giant section of the Kamdebooberge (Sneeuberg mountain complex, Eastern Cape, South Africa) has indicated that these mountains may be of significant conservation value. Accordingly, a precursory, rapid multi-disciplinary biodiversity assessment was undertaken in January 2011, focusing on plants, tetrapod vertebrates and leafhoppers. The botanical results confirm the Kamdebooberge as being of high botanical conservation value, hosting three strict endemics, healthy populations of five other Sneeuberg endemics, and fynbos communities comprising species not found elsewhere in the Sneeuberg. The Kamdebooberge are important for herpetofauna (excluding serpentoids) and mammals, hosting several range-restricted and regional endemics. The expedition uncovered three new leafhopper species, together with several species previously only known from the Cape Floristic Region. Further detailed faunal work may provide further interesting results from these mountains, which show a high conservation value unique to the southern Escarpment.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-1-56) contains supplementary material, which is available to authorized users.