Lessons from comparative analysis of X-chromosome inactivation in mammals

In most mammals, X-chromosome inactivation is used as the strategy to achieve dosage compensation between XX females and XY males. This process is developmentally regulated, resulting in the differential treatment of the two X chromosomes in the same nucleus and mitotic heritability of the silent state. A lack of dosage compensation in an XX embryo is believed to result in early lethality, at least in eutherians. Given its fundamental importance, X-chromosome inactivation would be predicted to be a highly conserved process in mammals. However, recent studies have revealed major mechanistic differences in X inactivation between eutherians and marsupials, suggesting that the evolution of the X chromosome as well as developmental differences between mammals have led to diverse evolutionary strategies for dosage compensation.     

Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates

The numbers of functional olfactory receptor (OR) genes in humans and mice are about 400 and 1,000 respectively. In both humans and mice, these genes exist as genomic clusters and are scattered over almost all chromosomes. The difference in the number of genes between the two species is apparently caused by massive inactivation of OR genes in the human lineage and a substantial increase of OR genes in the mouse lineage after the human–mouse divergence. Compared with mammals, fishes have a much smaller number of OR genes. However, the OR gene family in fishes is much more divergent than that in mammals. Fishes have many different groups of genes that are absent in mammals, suggesting that the mammalian OR gene family is characterized by the loss of many group genes that existed in the ancestor of vertebrates and the subsequent expansion of specific groups of genes. Therefore, this gene family apparently changed dynamically depending on the evolutionary lineage and evolved under the birth-and-death model of evolution. Study of the evolutionary changes of two gene families for vomeronasal receptors and two gene families for taste receptors, which are structurally similar, but remotely related to OR genes, showed that some of the gene families evolved in the same fashion as the OR gene family. It appears that the number and types of genes in chemosensory receptor gene families have evolved in response to environmental needs, but they are also affected by fortuitous factors.     

Sexual behavior, reproductive physiology and sperm competition in male mammals

Sperm competition involves competition between the gametes of two or more males of a species for fertilization of a given set of ova. Sperm competition is widespread among mammals, as in many other groups of vertebrates. Effects of sexual selection, via sperm competition, upon the evolution of reproductive physiology and behavior are much better understood in invertebrates (and especially in insects) than is the case for mammals. However, if the reproductive organs of male mammals are viewed as an integrated system for production and delivery of spermatozoa (and accessory glandular secretions) to females, then it is logical to assume that sperm competition might influence the evolution of all parts of the system, as well as associated physiological mechanisms (e.g., testicular endocrinology) and behavior (e.g., copulatory patterns). Here we analyze and review relationships between mating systems, relative testes sizes and sperm morphology, phallic morphology, circulating testosterone levels and sexual behavior in male mammals.     

Functional morphology and evolution of aspiration breathing in tetrapods

In the evolution of aspiration breathing, the responsibility for lung ventilation gradually shifted from the hyobranchial to the axial musculoskeletal system, with axial muscles taking over exhalation first, at the base of Tetrapoda, and then inhalation as well at the base of Amniota. This shift from hyobranchial to axial breathing freed the tongue and head to adapt to more diverse feeding styles, but generated a mechanical conflict between costal ventilation and high-speed locomotion. Some "lizards" (non-serpentine squamates) have been shown to circumvent this speed-dependent axial constraint with accessory gular pumping during locomotion, and here we present a new survey of gular pumping behavior in the tuatara and 40 lizard species. We observed gular pumping behavior in 32 of the 40 lizards and in the tuatara, indicating that the ability to inflate the lungs by gular pumping is a shared-derived character for Lepidosauria. Gular pump breathing in lepidosaurs may be homologous with buccal pumping in amphibians, but non-ventilatory buccal oscillation and gular flutter have persisted throughout amniote evolution and gular pumping may have evolved independently by modification of buccal oscillation. In addition to gular pumping in some lizards, three other innovations have evolved repeatedly in the major amniote clades to circumvent the speed-dependent axial constraint: accessory inspiratory muscles (mammals, crocodylians and turtles), changing locomotor posture (mammals and birds) and respiratory-locomotor phase coupling to reduce the mechanical conflict between aspiration breathing and locomotion (mammals and birds).     

Peptidoglycan recognition proteins (PGRPs)

Innate immune system recognizes microorganisms through a series of pattern recognition receptors that are highly conserved in evolution. Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules that are conserved from insects to mammals and recognize bacteria and their unique cell wall component, peptidoglycan (PGN). Drosophila, mosquito, and mammals have families of 13, 7, and 4 PGRP genes, respectively, and some of these genes are alternatively spliced. PGRPs are differentially expressed in various cells and tissues, their expression is often upregulated by bacteria, and they mediate host responses to bacterial infections. Insect PGRPs have four known effector functions that are unique for insects: activation of prophenoloxidase cascade, activation of Toll receptor, activation of Imd pathway, and induction of phagocytosis. One function, amidase activity, is shared by some insect and mammalian PGRPs, whereas antibacterial activity of some mammalian PGRPs is unique for mammals.     

Characterization of dopamine receptors in various species of invertebrates and vertebrates

Dopamine receptors can be characterized using [³H]spiroperidol binding in the brain of various animal species of vertebrates but are not detectable in nervous tissues of invertebrates. Among the mammals, considering the whole brain, the amount of dopamine receptor per unit of tissue decreases with increasing evolution. On the contrary, striatal dopamine receptor density is almost the same in the different mammalian brains examined. Dopamine receptor density in limbic areas increases from mice to monkeys.It is suggested that the enhancement of dopamine receptor density per unit of tissue in limbic areas parallels the degree of animal evolution.     

Primary structure and variation of the T-cell receptor delta-chain from a marsupial,Macropus eugenii

Although gammadelta T-cells form only a small portion of circulating T-cells in mice and humans, they are more frequent in many other types of mammals and this has lead to speculation regarding their roles and the evolutionary significance of their relative abundance. Moreover, whilst clear homologues of four types of T-cell receptor (TCR) chains (alpha, beta, delta and gamma) have been identified in vertebrates as distantly related as eutherian mammals and cartilaginous fish, there are still many gaps in our knowledge of these TCR components from various taxa. Such knowledge would further illuminate the evolution and function of these receptors and of gammadelta T-cells. Here, we report the molecular cloning of a TCR-delta chain cDNA from the tammar wallaby (Macropus eugenii) which represents the first component of the gammadelta TCR to be characterised from a marsupial. A PCR-based survey of variable (V) segment usage in tammar wallaby mammary-associated lymph node indicated that, although gammadelta T-cells may be sparse in this type of tissue, this species has at least three subfamilies of V genes that have been broadly conserved across vertebrate evolution. Two V subfamilies found in the tammar wallaby were relatively similar and may have diverged more recently, an event that probably occurred at some point in the marsupial lineage.     

On the evolution of X-chromosome inactivation in mammals and the clinical consequences to man—A hypothesis

A clinical analysis of abnormal sex chromosome states in man suggests that Lyon's recent X-Y translocation hypothesis for the evolution of X-chromosome inactivation in mammals most likely would have lead to an evolutionary dead-end. Therefore, as an alternate I have hypothesized that: X-chromosome inactivation in somatic cells of mammals could have evolved by a complementary process of one by one heterozygous physical deletion in males and heterozygous inactivation in females of genes for “somatic” traits scattered throughout the genome whose effective output had become 50% excessive during prior evolution. However, this complementary process could occur safely only if the genes so deleted or inactivated first segregated by chance onto the evolving sex-chromosomes via a one by one reciprocal exchange for non-sex related genes already there. The complementary process thereby would allow slow evolution of the Y-chromosome in the male and X-chromosome inactivation in the female. Evolution of X-chromosome inactivation in this manner is compatible with Ohno's observation of “conservation” of the X-chromosome in mammals; and the occurrance of clinical “somatic” abnormalities in the abnormal X or Y chromosome states of man despite X-chromosome inactivation.     

V(D)J recombination in zebrafish: Normal joining products with accumulation of unresolved coding ends and deleted signal ends

V(D)J recombination proceeds from a site-specific cleavage to an imprecise end joining, via generation and resolution of recombination ends. Although rearranged antigen receptor genes isolated from zebrafish (Danio rerio) resemble those made in mammals, differences may arise during evolution from lower to higher vertebrates, in regard to efficiency, fidelity and regulation of this recombination. To elucidate the V(D)J recombination reaction in zebrafish, we characterized recombination ends transiently produced by zebrafish lymphocytes, as well as joining products. Similar to their mammalian counterpart, zebrafish lymphocytes make perfect signal joints and normal coding joints, indicating their competent end resolution machinery. However, recombination ends recovered from the same zebrafish lymphoid tissues exhibit some features that are not readily seen in normal mammalian counterpart: deleted signal ends and accumulation of opened coding ends. These results indicate that the recombination reaction in zebrafish lymphocytes is inefficient and less stringently regulated, which may result from unstable post-cleavage complexes, and/or slow transition from cleavage to resolution. Our data suggests that the V(D)J recombination machinery may have undergone evolution selection to become more efficient in higher jawed vertebrates.     

From fish to modern humans--comparative anatomy, homologies and evolution of the head and neck musculature

In a recent paper Diogo (2008) reported the results of the first part of an investigation of the comparative anatomy, homologies and evolution of the head and neck muscles of osteichthyans (bony fish + tetrapods). That report mainly focused on actinopterygian fish, but also compared these fish with certain non-mammalian sarcopterygians. The present paper focuses mainly on sarcopterygians, and particularly on how the head and neck muscles have evolved during the transitions from sarcopterygian fish and non-mammalian tetrapods to monotreme and therian mammals, including modern humans. The data obtained from our dissections of the head and neck muscles of representative members of sarcopterygian fish, amphibians, reptiles, monotremes and therian mammals, such as rodents, tree-shrews, colugos and primates, including modern humans, are compared with the information available in the literature. Our observations and comparisons indicate that the number of mandibular and true branchial muscles (sensu this work) present in modern humans is smaller than that found in mammals such as tree-shrews, rats and monotremes, as well as in reptiles such as lizards. Regarding the pharyngeal musculature, there is an increase in the number of muscles at the time of the evolutionary transition leading to therian mammals, but there was no significant increase during the transition leading to the emergence of higher primates and modern humans. The number of hypobranchial muscles is relatively constant within the therian mammals we examined, although in this case modern humans have more muscles than other mammals. The number of laryngeal and facial muscles in modern humans is greater than that found in most other therian taxa. Interestingly, modern humans possess peculiar laryngeal and facial muscles that are not present in the majority of the other mammalian taxa; this seems to corroborate the crucial role played by vocal communication and by facial expressions in primate and especially in human evolution. It is hoped that by compiling, in one paper, data about the head and neck muscles of a wide range of sarcopterygians, the present work could be useful to comparative anatomists, evolutionary biologists and functional morphologists and to researchers working in other fields such as developmental biology, genetics and/or evolutionary developmental biology.     

Comparative genome maps of the pangolin, hedgehog, sloth, anteater and human revealed by cross-species chromosome painting: further insight into the ancestral karyotype and genome evolution of eutherian mammals

To better understand the evolution of genome organization of eutherian mammals, comparative maps based on chromosome painting have been constructed between human and representative species of three eutherian orders: Xenarthra, Pholidota, and Eulipotyphla, as well as between representative species of the Carnivora and Pholidota. These maps demonstrate the conservation of such syntenic segment associations as HSA3/21, 4/8, 7/16, 12/22, 14/15 and 16/19 in Eulipotyphla, Pholidota and Xenarthra and thus further consolidate the notion that they form part of the ancestral karyotype of the eutherian mammals. Our study has revealed many potential ancestral syntenic associations of human chromosomal segments that serve to link the families as well as orders within the major superordinial eutherian clades defined by molecular markers. The HSA2/8 and 7/10 associations could be the cytogenetic signatures that unite the Xenarthrans, while the HSA1/19p could be a putative signature that links the Afrotheria and Xenarthra. But caution is required in the interpretation of apparently shared syntenic associations as detailed analyses also show examples of apparent convergent evolution that differ in breakpoints and extent of the involved segments.     

The avian Toll-Like receptor pathway—Subtle differences amidst general conformity

The Toll-Like receptor (TLR) pathway plays a core role in innate immunity and is maintained with remarkable consistency across all vertebrate species. Amidst this background of overall conservation, subtle differences in the components that make up this pathway may have important implications for species-specific defense against key pathogens. Here we employ a homology-based comparative method to characterize the TLR pathway in the recently sequenced chicken and zebra finch genomes, which represent two distantly related bird species. The key features of the TLR pathway are conserved in birds and mammals, although some clear differences exist. The TLR receptors show a pattern of gene duplication and gene loss in both avian species when compared to mammals. In particular, we observe avian specific duplication of both TLR1 and TLR2 as well and a recent duplication of the TLR7 gene in the zebra finch lineage. Both positive selection and gene conversion shape the evolution of the avian specific TLR2 genes. In addition, there are notable differences in the zebra finch repertoire of antimicrobial peptides (AMPs) when compared to those of the chicken. Bioinformatic analysis reveals no evidence of cathelicidins in the zebra finch genome but does identify a cluster of 12 novel defensins which map to the avian beta-defensin locus on chromosome 3. These findings contribute to the characterization of the differing immune response systems that have evolved in individual vertebrate species in response to their microbiological environment.     

Teleost IgSF immunoregulatory receptors

In all animals innate immunity is the first line of immune defense from invading pathogens. The prototypical innate cellular responses such as phagocytosis, degranulation, and cellular cytotoxicity are elicited by leukocytes in a diverse range of animals including fish, amphibians, birds and mammals reinforcing the importance of such primordial defense mechanisms. In mammals, these responses are intricately controlled and coordinated at the cellular level by distinct subsets of immunoregulatory receptors. Many of these surface proteins belong to the immunoglobulin superfamily and in mammals elaborate immunoregulatory receptor networks play a major role in the control of infectious diseases. Recent examination of teleost immunity has begun to further illustrate the complexities of these receptor networks in lower vertebrates. However, little is known about the mechanisms that control how immunoregulatory receptors influence cellular decision making in ectothermic vertebrates. This review focuses on several families of recently discovered immunoglobulin superfamily members in fish that share structural, phylogenetic and in some cases functional relationships with mammalian immunoregulatory receptors. Further characterization of these teleost innate immune receptor families will provide detailed information regarding the conservation and importance of innate immune defense strategies throughout vertebrate evolution.     

Teleost IgSF immunoregulatory receptors

In all animals innate immunity is the first line of immune defense from invading pathogens. The prototypical innate cellular responses such as phagocytosis, degranulation, and cellular cytotoxicity are elicited by leukocytes in a diverse range of animals including fish, amphibians, birds and mammals reinforcing the importance of such primordial defense mechanisms. In mammals, these responses are intricately controlled and coordinated at the cellular level by distinct subsets of immunoregulatory receptors. Many of these surface proteins belong to the immunoglobulin superfamily and in mammals elaborate immunoregulatory receptor networks play a major role in the control of infectious diseases. Recent examination of teleost immunity has begun to further illustrate the complexities of these receptor networks in lower vertebrates. However, little is known about the mechanisms that control how immunoregulatory receptors influence cellular decision making in ectothermic vertebrates. This review focuses on several families of recently discovered immunoglobulin superfamily members in fish that share structural, phylogenetic and in some cases functional relationships with mammalian immunoregulatory receptors. Further characterization of these teleost innate immune receptor families will provide detailed information regarding the conservation and importance of innate immune defense strategies throughout vertebrate evolution.     

Evolutionary divergence of thyrotropin receptor structure

The availability of 18 thyrotropin receptor (TSHR) sequences, including two recent entries for primates and seven from fish, have allowed us to investigate diversification of residues or domains during evolution. We used a likelihood ratio test for evolutionary rate shifts [Proc. Natl. Acad. Sci. 98 (2001) 14512] using LH/CGR sequences as an out-group. At each residue in the alignment, a statistical test was performed for a rate shift at the divergence between mammals and fish. Eighty-two rate shift sites were found, significantly more than was expected (p < 0.0001). The occurrence of rate shifts was highest in the intracellular tail, lowest in the transmembrane serpentine and intermediate in the ectodomain. In 52 mammalian sites, the rates were significantly faster than for the corresponding sites in fish. We have identified rate shift in sites important to TSHR function or in intimate proximity to such regions. The former category includes residues 53 and 55 (of LLR1 beta strand) and 253 and 255 (of LLR9 beta strand), crucial to TSH thyrotropic activity, residue 113, the site of N-linked glycosylation limited to humans, residue 310, an important switch in the hinge region for receptor binding and constitutive activity and residue 382 which centres a motif important for TSH-mediated receptor activation. The rate shifts positions close to functional region include a site proximal to a TSHR-specific motif on LLR3 beta strand, sites important in TM helix structure and homodimerization as well as, in the case of the third intracellular loop, to TSHR/G protein coupling. Rate shift analyses have identified residues whose manipulation in the human TSHR may lead to better understanding of receptor functions and help in the creation of designer analogues.     

Evolution and function of chemokine receptors in the immune system of lower vertebrates

Chemokine receptors and their counterpart ligands are one of the evolutionary innovations of vertebrates. They play a guiding role in the coordination of cell trafficking in many biological processes. Comparative syntenic and phylogenetic analyses provide insight into the evolution of chemokine receptors and suggest that the repertoire of chemokine receptors varies in each species, regardless of the evolutionary position of the species. Despite the rapid evolution of chemokine receptors, the expression and function of orthologous chemokine receptors in lower and higher vertebrates are very similar. This is also true for the chemokine ligands that have been examined so far, such as CXCL8, CXCL12, and CCL25. As examples, this review will discuss how the evolution of the chemokine receptor CXCR4 is coincident with the emergence of lymphocytes in jawless vertebrates (lamprey); and that, in jawed vertebrates, CXCR4 and CCR9 are involved in thymus colonization. In myeloid cells, the function of CXCR1 in neutrophils and the expression of CXCR3 in macrophages and DCs are evolutionarily conserved between fish and mammals. In this context, medaka and zebrafish are outstanding models for studying the function of chemokines and their receptors.     

Seasonal and Ontogenetic Variation in Subcutaneous Adipose Of the Bowhead Whale (Balaena mysticetus)

Cetacean evolution was shaped by an extraordinary land‐to‐sea transition in which the ancestors of whales became fully aquatic. As part of this transition, these mammals evolved unusually thick blubber which acts as a metabolic reservoir as well as an insulator and provides buoyancy and streamlining. This study describes blubber stratification and correlates it to seasonal variation, feeding patterns, and ontogeny in an arctic‐adapted mysticete, the bowhead whale (Balaena mysticetus). Bowheads are unique among mammals for possessing the largest known blubber stores. We found that adipocyte numbers in bowheads, like other mammals, do not vary with season or feeding pattern but that adipocyte size and structural fiber densities do vary with blubber depth. Anat Rec, 298:1416–1423, 2015. © 2015 Wiley Periodicals, Inc.     

Longevity and the evolution of the mitochondrial DNA-coded proteins in mammals

The amino acids sequences of the mitochondrial DNA-coded peptides of placental mammals evolved at different rates in different branches of the mammalian phylogenetic tree. Adaptive selection was suggested to account for the faster evolution of some mitochondrial DNA-coded proteins in several branches of the mammalian tree, but the driving force(s) for the accelerated evolution has not been elucidated. Mitochondria generate reactive oxygen species (ROS) that appear to constrain the life span of many species. Therefore, I tested the hypothesis that the evolution of mammalian longevity drives the accelerated evolution of mitochondrial DNA-coded peptides. Using rodents as an outgroup for a clad that included most placental mammals (excluding rodents and hedgehogs) the computed rates of amino acid substitution per site were positively correlated with genus longevity (maximal observed averaged life span) for most of the mitochondrial DNA-coded peptides. The substitution per site of ATP6, the proton conducting subunit of ATPsynthase, CYTB, the core subunit of ubiquinone oxidoreductase that participate in both electron and proton transport, and ND3, a subunit of NADH dehydrogenase, showed the strongest correlations with longevity. Additional confirmation for the hypothesis was obtained by the observation that the genetic distances between placental mammals species that belong to different orders are positively correlated with the sum of longevities of the species pairs. The substitutions per site for the entire amino acid sequence coded by the heavy strand mtDNA were also positively correlated with the average longevities of the placental mammals orders. These results support the hypothesis that the evolution of longevity in mammals drove the accelerated evolution of mtDNA-coded peptide. It is suggested that, in mammals, adaptive selection of mutations that decrease the rate of production of reactive oxygen species, directly or indirectly (e.g. by increasing proton leak), increases longevity.     

Role of neurokinin receptors and ionic mechanisms within the respiratory network of the lamprey

We have suggested that in the lamprey, a medullary region called the paratrigeminal respiratory group (pTRG), is essential for respiratory rhythm generation and could correspond to the pre-Bötzinger complex (pre-BötC), the hypothesized kernel of the inspiratory rhythm-generating network in mammals. The present study was performed on in vitro brainstem preparations of adult lampreys to investigate whether some functional characteristics of the respiratory network are retained throughout evolution and to get further insights into the recent debated hypotheses on respiratory rhythmogenesis in mammals, such as for instance the “group-pacemaker” hypothesis. Thus, we tried to ascertain the presence and role of neurokinins (NKs) and burst-generating ion currents, such as the persistent Na⁺ current (I_NaP) and the Ca²⁺-activated non-specific cation current (I_CAN), described in the pre-Bötzinger complex. Respiratory activity was monitored as vagal motor output. Substance P (SP) as well as NK1, NK2 and NK3 receptor agonists (400–800 nM) applied to the bath induced marked increases in respiratory frequency. Microinjections (0.5–1 nl) of SP as well as the other NK receptor agonists (1 μM) into the pTRG increased the frequency and amplitude of vagal bursts. Riluzole (RIL) and flufenamic acid (FFA) were used to block I_NaP and I_CAN, respectively. Bath application of either RIL or FFA (20–50 μM) depressed, but did not suppress respiratory activity. Coapplication of RIL and FFA at 50 μM abolished the respiratory rhythm that, however, was restarted by SP microinjected into the pTRG. The results show that NKs may have a modulatory role in the lamprey respiratory network through an action on the pTRG and that I_NaP and I_CAN may contribute to vagal burst generation. We suggest that the “group-pacemaker” hypothesis is tenable for the lamprey respiratory rhythm generation since respiratory activity is abolished by blocking both I_NaP and I_CAN, but is restored by enhancing network excitability.     

The in vitro and in ovo responses of chickens to TLR9 subfamily ligands

Although Toll-like receptors (TLRs) have been well characterised in mammals, less work has been carried out in non-mammalian species, such as chickens. In this study the response of chicken cells to the TLR9 subfamily of ligands was characterised in vitro and in ovo. It was found that even though chickens appear to have only one functional receptor to represent the TLR9 subfamily, stimulation of chicken splenocytes with TLR7 and TLR9 ligands induced proinflammatory cytokine production and cell proliferation, similar to that observed when the homologous mammalian receptors are stimulated. Furthermore, we demonstrated that the in ovo administration of these TLR ligands elicits a response, such as cytokine production, that can be detected post-hatch. The current knowledge of the action of TLR ligands in mammals, in conjunction with their immunomodulating ability shown in this study, draws attention to their potential use as therapeutic agents for the poultry industry.