Environmental influences in the evolution of tetrapod hearing sensitivity and middle ear tuning

Vertebrates inhabit and communicate acoustically in most natural environments. We review the influence of environmental factors on the hearing sensitivity of terrestrial vertebrates, and on the anatomy and mechanics of the middle ears. Evidence suggests that both biotic and abiotic environmental factors affect the evolution of bandwidth and frequency of peak sensitivity of the hearing spectrum. Relevant abiotic factors include medium type, temperature, and noise produced by nonliving sources. Biotic factors include heterospecific, conspecific, or self-produced sounds that animals are selected to recognize, and acoustic interference by sounds that other animals generate. Within each class of tetrapods, the size of the middle ear structures correlates directly to body size and inversely to frequency of peak sensitivity. Adaptation to the underwater medium in cetaceans involved reorganization of the middle ear for novel acoustic pathways, whereas adaptation to subterranean life in several mammals resulted in hypertrophy of the middle ear ossicles to enhance their inertial mass for detection of seismic vibrations. The comparative approach has revealed a number of generalities about the effect of environmental factors on hearing performance and middle ear structure across species. The current taxonomic sampling of the major tetrapod groups is still highly unbalanced and incomplete. Future expansion of the comparative evidence should continue to reveal general patterns and novel mechanisms.     

Patterns and processes in the evolution of the eukaryotic endomembrane system

The eukaryotic endomembrane system (ES) is served by hundreds of dedicated proteins. Experimental characterization of the ES-associated molecular machinery in several model eukaryotes complemented by a recent progress in phylogenomics and comparative genomics have revealed a conserved complex core of the machinery that appears to have been established before the last eukaryotic common ancestor (LECA). At the same time, modern eukaryotes exhibit a huge variation in the ES resulting from a multitude of evolutionary processes operating along the ever-branching paths from the LECA to its descendants. The most important source of evolutionary novelty in the ES functioning has undoubtedly been gene duplication followed by divergence of the gene copies, responsible not only for the pre-LECA establishment of many multi-paralog families of proteins in the very core of the ES-associated machinery, but also for post-LECA lineage-specific elaborations via family expansions and the origin of novel components. Extreme sequence divergence has obscured actual homologous relationships between potentially many components of the machinery, even between orthologous proteins, as illustrated by the yeast Vps51 subunit of the vesicle tethering complex GARP hypothesized here to be a highly modified ortholog of a conserved eukaryotic family typified by the zebrafish Fat-free (Ffr) protein. A dynamic evolution of many ES-associated proteins, especially those centred around RAB and ARF GTPases, seems to take place at the level of their domain architectures. Finally, reductive evolution and recurrent gene loss are emerging as pervasive factors shaping the ES in all phylogenetic lineages.     

Patterns and processes in the evolution of the eukaryotic endomembrane system

Abstract

The eukaryotic endomembrane system (ES) is served by hundreds of dedicated proteins. Experimental characterization of the ES-associated molecular machinery in several model eukaryotes complemented by a recent progress in phylogenomics and comparative genomics have revealed a conserved complex core of the machinery that appears to have been established before the last eukaryotic common ancestor (LECA). At the same time, modern eukaryotes exhibit a huge variation in the ES resulting from a multitude of evolutionary processes operating along the ever-branching paths from the LECA to its descendants. The most important source of evolutionary novelty in the ES functioning has undoubtedly been gene duplication followed by divergence of the gene copies, responsible not only for the pre-LECA establishment of many multi-paralog families of proteins in the very core of the ES-associated machinery, but also for post-LECA lineage-specific elaborations via family expansions and the origin of novel components. Extreme sequence divergence has obscured actual homologous relationships between potentially many components of the machinery, even between orthologous proteins, as illustrated by the yeast Vps51 subunit of the vesicle tethering complex GARP hypothesized here to be a highly modified ortholog of a conserved eukaryotic family typified by the zebrafish Fat-free (Ffr) protein. A dynamic evolution of many ES-associated proteins, especially those centred around RAB and ARF GTPases, seems to take place at the level of their domain architectures. Finally, reductive evolution and recurrent gene loss are emerging as pervasive factors shaping the ES in all phylogenetic lineages.     

Evolution of the tetrapod ear: an analysis and reinterpretation

The dominant view of tetrapod otic evolution–the “standard view”–holds that the tympanum developed very early in tetrapod history and is homologous in all tetrapods and that the opercular process of the rhipidistian hyomandibula is homologous to the tympanic process of the stapes in lower tetrapods. Under that view, the labyrinthodont amphibians of the Paleozoic are usually considered ancestral to reptiles, and thus the “otic notch” of labyrinthodonts and the tympanum it presumably contained form the starting-point for middle ear evolution in reptiles. Four problems have classically been identified with the standard view: the differing relationships of the internal mandibular branch of N. VII (chorda tympani) to the processes of the stapes in amniotes and anurans; the differing orientations of the stapes in key fossil and living groups; the location of the tympanum in early fossil reptiles; and the transferral of the tympanum, during the origin of mammals, from the stapes to the articular bone of the lower jaw. An examination of these problems and of the solutions proposed under the standard view reveals the ad hoc, and therefore unsatisfactory, nature of the proposed solutions. To organize and review alternative hypotheses of otic evolution an analytical table is constructed, using three characters (tympanic process, Nerve VII, tympanum), each with two possible states. A total of eight hypotheses about middle ear evolution are possible under this system, one of which is the standard view. The seven “non-standard” hypotheses, only five of which have been argued in the literature, are briefly examined. Six of the “non-standard” hypotheses appear unattractive for various reasons, including reliance on ad hoc arguments. The seventh was first proposed by Gaupp in 1898. It is today almost universally ignored but apparently largely for historical rather than scientific reasons. This hypothesis, her called the “alternative view”, appears to rest on assumptions equally as plausible as those of the standard view. Moreover, it offers a solution of the problems associated with the standard view without, apparently, raising any similarly serious problems. This paper compares the standard and alternative views of middle ear evolution in detail. Comparison proceeds on two levels. On one level, they are compared in terms of the hypotheses of phyletic tetrapod relationships each promotes and how strongly each supports its hypothesis. Both views promote the same hypothesis of tetrapod relationships. The alternative view is the more parsimonious, but the difference is not considered sufficient to provide a choice. On another level, the two views are compared in terms of their implications for: (1) the evolution of relative and absolute auditory perceptive ability; (2) the origin of reptiles; (3) the evolution of the suspensorium and cranial kinesis; and (4) the origin and evolution of recent amphibians. The nature of the data required for a test of the implications of the two views is specified in each case. Where data are available. the alternative view is consistent and the standard view is inconsistent with these data. We conclude that the alternative view is the preferable hypothesis of middle-ear evolution. This conclusion implies the following: the tympanic membranes and the tympanic processes of the stapes in recent mammals, reptiles + birds. and frogs. are not homologous; the evolution of “special periotic systems” in the ancestors of amphibians and amniotes were independent events and preceded the evolution of tympanic membranes; the amphibian tympanic membrane. probably including that of labyrinthodonts. is not ancestral to that of amniotes. and that labyiinthodonts with an otic notch are not suitable as amniote ancestors; the stapes of early reptiles functioned primarily as part of the jaw suspension rather than in hearing; the mechanisms and abilities of sound perception in recent tetrapods are likely to be diverse rather than forming parts of a cline; and the lack of a tympanum in Gymnophiona and Caudata may be a retention of a primitive condition.     

Biogeography of Triassic tetrapods: evidence for provincialism and driven sympatric cladogenesis in the early evolution of modern tetrapod lineages

Triassic tetrapods are of key importance in understanding their evolutionary history, because several tetrapod clades, including most of their modern lineages, first appeared or experienced their initial evolutionary radiation during this Period. In order to test previous palaeobiogeographical hypotheses of Triassic tetrapod faunas, tree reconciliation analyses (TRA) were performed with the aim of recovering biogeographical patterns based on phylogenetic signals provided by a composite tree of Middle and Late Triassic tetrapods. The TRA found significant evidence for the presence of different palaeobiogeographical patterns during the analysed time spans. First, a Pangaean distribution is observed during the Middle Triassic, in which several cosmopolitan tetrapod groups are found. During the early Late Triassic a strongly palaeolatitudinally influenced pattern is recovered, with some tetrapod lineages restricted to palaeolatitudinal belts. During the latest Triassic, Gondwanan territories were more closely related to each other than to Laurasian ones, with a distinct tetrapod fauna at low palaeolatitudes. Finally, more than 75 per cent of the cladogenetic events recorded in the tetrapod phylogeny occurred as sympatric splits or within-area vicariance, indicating that evolutionary processes at the regional level were the main drivers in the radiation of Middle and Late Triassic tetrapods and the early evolution of several modern tetrapod lineages.     

Perspectives on the convergent evolution of tetrapod salt glands

Since their discovery in 1958, the function of specialized salt-secreting glands in tetrapods has been studied in great detail, and such studies continue to contribute to a general understanding of transport mechanisms of epithelial water and ions. Interestingly, during that same time period, there have been only few attempts to understand the convergent evolution of this tissue, likely as a result of the paucity of taxonomic, embryological, and molecular data available. In this review, we synthesize the available data regarding the distribution of salt glands across extant and extinct tetrapod lineages and the anatomical position of the salt gland in each taxon. Further, we use these data to develop hypotheses about the various factors that have influenced the convergent evolution of salt glands across taxa with special focus on the variation in the anatomical position of the glands and on the molecular mechanisms that may have facilitated the development of a salt gland by co-option of a nonsalt-secreting ancestral gland. It is our hope that this review will stimulate renewed interest in the topic of the convergent evolution of salt glands and inspire future empirical studies aimed at evaluating the hypotheses we lay out herein.     

The hyomandibular of Eusthenopteron foordi Whiteaves (Pisces: Crossopterygii) and the early evolution of the tetrapod stapes

The hyomandibular of Eusthenopteron foordi Whiteaves is briefly described and an attempt is made to reconcile discrepancies between previous accounts. The course of the branches of the truncus hyoideo-mandibularis (facial nerve VII) is discussed. The early evolution of the tetrapod stapes is considered in connection with the uncoupling of the head from the trunk and subsequent reduction in size ot the semicircular canals. The principal morphological character which distinguishes the stapes from the hyomandibular is found to be related to the course of the orbital (stapedial) artery and the truncus hyoideo-mandibularis.     

Some aspects of the origin and early evolution of bioenergetic processes

Model experiments demonstrating some possibilities of the primitive bioenergetics were performed. Comparing the catalytic properties of heme and hemoproteinoid in electron transfer reactions, it was shown that hemin acts as an active dark catalyst, whereas hemoproteinoid is a photosensitizer of these processes. The heme-containing enzyme, peroxidase/or even the hemoproteinoid/is also able to provide the phosphorylation of different substrates. It is proposed, that the phosphorylation is initiated by a hydroxyl radical occuring in the peroxidase reaction. We believe that those reactions could play a role in prebiotic energetics by coupling the electron transfer with the phosphorylation of suitable substrates.     

Some aspects of the origin and early evolution of bioenergetic processes

Model experiments demonstrating some possibilities of the primitive bioenergetics were performed. Comparing the catalytic properties of heme and hemoproteinoid in electron transfer reactions, it was shown that hemin acts as an active dark catalyst, whereas hemoproteinoid is a photosensitizer of these processes. The heme-containing enzyme, peroxidase [or even the hemoproteinoid] is also able to provide the phosphorylation of different substrates. It is proposed, that the phosphorylation is initiated by a hydroxyl radical occuring in the peroxidase reaction. We believe that those reactions could play a role in prebiotic energetics by coupling the electron transfer with the phosphorylation of suitable substrates.     

Uricoteley:its nature and origin during the evolution of tetrapod vertebrates

The hepatic mechanism for detoxication of ammonia formed during amino acid gluconeogenesis in uricotelic vertebrates requires the intramitochondrial synthesis of glutamine by glutamine synthetase. This glutamine then serves as a precursor of uric acid in the cytosol. The evolutionary development of uricoteley thus required the localization of glutamine synthetase in liver mitochondria. The mechanism for the mitochondrial import of glutamine synthetase in uricotelic vertebrate liver is not yet known. Tortoises, extant relatives of the stem reptiles, possess both the ureotelic and uricotelic hepatic systems. It therefore seems likely that the genetic events allowing the mitochondrial localization of glutamine synthetase in liver occurred in the amniote amphibian ancestors of the stem reptiles. The selection of ureoteley by the theropsids and of uricoteley by the sauropsids were major events in the divergence and subsequent evolution of these two lines. Once established in the sauropsid line, uricoteley has persisted through to the higher reptiles, crocodilians, and birds. Uricoteley was in part responsible for the radiation of the archosaurs during the Triassic as a water-conserving mechanism in the adult, thereby allowing them to invade the arid environments of that period. Contrary to dogma, uricoteley was probably of minor significance in the development of the cleidoic egg. Neither mammalian nor avian embryonic liver tissues catabolize amino acids to any great extent, so it is inappropriate to attribute to them a kind of "waste" nitrogen metabolism.     

Pattern of the divergence of olfactory receptor genes during tetrapod evolution

The olfactory receptor (OR) multigene family is responsible for the sense of smell in vertebrate species. OR genes are scattered widely in our chromosomes and constitute one of the largest gene families in eutherian genomes. Some previous studies revealed that eutherian OR genes diverged mainly during early mammalian evolution. However, the exact period when, and the ecological reason why eutherian ORs strongly diverged has remained unclear. In this study, I performed a strict data mining effort for marsupial opossum OR sequences and bootstrap analyses to estimate the periods of chromosomal migrations and gene duplications of OR genes during tetrapod evolution. The results indicate that chromosomal migrations occurred mainly during early vertebrate evolution before the monotreme-placental split, and that gene duplications occurred mainly during early mammalian evolution between the bird-mammal split and marsupial-placental split, coinciding with the reduction of opsin genes in primitive mammals. It could be thought that the previous chromosomal dispersal allowed the OR genes to subsequently expand easily, and the nocturnal adaptation of early mammals might have triggered the OR gene expansion.     

Patterns of mechanical energy change in tetrapod gait: pendula, springs and work

Kinematic and center of mass (CoM) mechanical variables used to define terrestrial gaits are compared for various tetrapod species. Kinematic variables (limb phase, duty factor) provide important timing information regarding the neural control and limb coordination of various gaits. Whereas, mechanical variables (potential and kinetic energy relative phase, %Recovery, %Congruity) provide insight into the underlying mechanisms that minimize muscle work and the metabolic cost of locomotion, and also influence neural control strategies. Two basic mechanisms identified by Cavagna et al. (1977. Am J Physiol 233:R243-R261) are used broadly by various bipedal and quadrupedal species. During walking, animals exchange CoM potential energy (PE) with kinetic energy (KE) via an inverted pendulum mechanism to reduce muscle work. During the stance period of running (including trotting, hopping and galloping) gaits, animals convert PE and KE into elastic strain energy in spring elements of the limbs and trunk and regain this energy later during limb support. The bouncing motion of the body on the support limb(s) is well represented by a simple mass-spring system. Limb spring compliance allows the storage and return of elastic energy to reduce muscle work. These two distinct patterns of CoM mechanical energy exchange are fairly well correlated with kinematic distinctions of limb movement patterns associated with gait change. However, in some cases such correlations can be misleading. When running (or trotting) at low speeds many animals lack an aerial period and have limb duty factors that exceed 0.5. Rather than interpreting this as a change of gait, the underlying mechanics of the body's CoM motion indicate no fundamental change in limb movement pattern or CoM dynamics has occurred. Nevertheless, the idealized, distinctive patterns of CoM energy fluctuation predicted by an inverted pendulum for walking and a bouncing mass spring for running are often not clear cut, especially for less cursorial species. When the kinematic and mechanical patterns of a broader diversity of quadrupeds and bipeds are compared, more complex patterns emerge, indicating that some animals may combine walking and running mechanics at intermediate speeds or at very large size. These models also ignore energy costs that are likely associated with the opposing action of limbs that have overlapping support times during walking. A recent model of terrestrial gait (Ruina et al., 2005. J Theor Biol, in press) that treats limb contact with the ground in terms of collisional energy loss indicates that considerable CoM energy can be conserved simply by matching the path of CoM motion perpendicular to limb ground force. This model, coupled with the earlier ones of pendular exchange during walking and mass-spring elastic energy savings during running, provides compelling argument for the view that the legged locomotion of quadrupeds and other terrestrial animals has generally evolved to minimize muscle work during steady level movement.     

Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing.     

Hedgehog regulation of superficial slow muscle fibres in Xenopus and the evolution of tetrapod trunk myogenesis

In tetrapod phylogeny, the dramatic modifications of the trunk have received less attention than the more obvious evolution of limbs. In somites, several waves of muscle precursors are induced by signals from nearby tissues. In both amniotes and fish, the earliest myogenesis requires secreted signals from the ventral midline carried by Hedgehog (Hh) proteins. To determine if this similarity represents evolutionary homology, we have examined myogenesis in Xenopus laevis, the major species from which insight into vertebrate mesoderm patterning has been derived. Xenopus embryos form two distinct kinds of muscle cells analogous to the superficial slow and medial fast muscle fibres of zebrafish. As in zebrafish, Hh signalling is required for XMyf5 expression and generation of a first wave of early superficial slow muscle fibres in tail somites. Thus, Hh-dependent adaxial myogenesis is the likely ancestral condition of teleosts, amphibia and amniotes. Our evidence suggests that midline-derived cells migrate to the lateral somite surface and generate superficial slow muscle. This cell re-orientation contributes to the apparent rotation of Xenopus somites. Xenopus myogenesis in the trunk differs from that in the tail. In the trunk, the first wave of superficial slow fibres is missing, suggesting that significant adaptation of the ancestral myogenic programme occurred during tetrapod trunk evolution. Although notochord is required for early medial XMyf5 expression, Hh signalling fails to drive these cells to slow myogenesis. Later, both trunk and tail somites develop a second wave of Hh-independent slow fibres. These fibres probably derive from an outer cell layer expressing the myogenic determination genes XMyf5, XMyoD and Pax3 in a pattern reminiscent of amniote dermomyotome. Thus, Xenopus somites have characteristics in common with both fish and amniotes that shed light on the evolution of somite differentiation. We propose a model for the evolutionary adaptation of myogenesis in the transition from fish to tetrapod trunk.     

Patterns in the evolution of amentiferous fruits

The diversity of fruit types within the Amentiferae appears to be the result of different seed dispersal and seedling establishment strategies that have evolved independently in the amentiferous families within the confines imposed by the wind-pollination syndrome. Dispersal of unadorned fruits and seeds by wind (e.g.,Betula, Rhoiptelea, Casuarina) has preceded the development of more efficient air-borne devices (e.g.,Ostrya, Carpinus, Engelhardia). Animal dispersal is the most advanced strategy, relying rarely on drupes, as in the shrubby Myricaceae, or on nuts, as inCorylus, Quercus, Carya, Juglans, Alfaroa, etc. The pattern of seedling establishment shows a structural-functional relationship to the seeddispersal strategy. Epigeal germination predominates in plants of open habitats. Those species with small fruits rely on wind dispersal, and their seeds have a relatively short germination time, whereas species with medium-sized fruits are often animal-dispersed with seeds that may have protracted germination times. In either case the reserve food supply for the young seedling is limited, and light is needed to spark photosynthesis. Hypogeal germination has evolved independently in several amentiferous families (e.g., Betulaceae, Fagaceae, Juglandaceae). This pattern is associated with closed habitats and plants with large seeds that have the capability of establishing vigorous seedlings in microhabitats of reduced light intensity where photosynthesis is impaired. The subterranean protection afforded the cotyledons and axillary meristems is a correlative feature that may have considerable importance in seedling survival where desiccation and predation are intense.