Adaptive Evolution of the Hox Gene Family for Development in Bats and Dolphins

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.     

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, both of which are associated with non-syndromic hearing loss in mammals. These genes were amplified and sequenced from a number of mammalian species, including echolocating and non-echolocating bats and whales, and were analysed together with published sequences. Sections of both genes showed phylogenetic signals that conflicted with accepted species relationships, with coding regions uniting laryngeal echolocating bats in a monophyletic clade. Bayesian estimates of posterior probabilities of convergent and divergent substitutions provided more direct evidence of sequence convergence between the two groups of laryngeal echolocating bats as well as between echolocating bats and dolphins. We found strong evidence of positive selection acting on some echolocating bat species and echolocating cetaceans, contrasting with purifying selection on non-echolocating bats. Signatures of sequence convergence and molecular adaptation in two additional hearing genes suggest that the acquisition of high-frequency hearing has involved multiple loci.     

Metabolism during flight in two species of bats, Phyllostomus hastatus and Pteropus gouldii.

The energetic cost of flight in a wind-tunnel was measured at various combinations of speed and flight angle from two species of bats whose body masses differ by almost an order of magnitude. The highest mean metabolic rate per unit body mass measured from P. hastatus (mean body mass, 0.093 kg) was 130.4 Wkg-1, and that for P. gouldii (mean body mass, 0.78 kg) was 69.6 Wkg-1. These highest metabolic rates, recorded from flying bats, are essentially the same as those predicted for flying birds of the same body masses, but are from 2.5 to 3.0 times greater than the highest metabolic rates of which similar-size exercising terrestrial mammals appear capable. The lowest mean rate of energy utilization per unit body mass P. hastatus required to sustain level flight was 94.2 Wkg-1 and that for P. gouldii was 53.4 Wkg-1. These data from flying bats together with comparable data for flying birds all fall along a straight line when plotted on double logarithmic coordinates as a function of body mass. Such data show that even the lowest metabolic requirements of bats and birds during level flight are about twice the highest metabolic capabilities of similar-size terrestrial mammals. Flying bats share with flying birds the ability to move substantially greater distance per unit energy consumed than walking or running mammals. Calculations show that P. hastatus requires only one-sixth the energy to cover a given distance as does the same-size terrestrial mammal, while P. gouldii requires one-fourth the energy of the same-size terrestrial mammal. An empirically derived equation is presented which enables one to make estimates of the metabolic rates of bats and birds during level flight in nature from body mass data alone. Metabolic data obtained in this study are compared with predictions calculated from an avian flight theory.     

鲸类低氧耐受的分子机制初探:基于HIF1α和TSC1基因的生物信息学分析

鲸类(Cetacea)具有超强潜水能力,长时间潜水造成的体内低氧是其适应完全水生生活面临的挑战之一.为了克服体内低氧环境,鲸类产生了一系列低氧耐受相关的解剖和生理等方面的适应特征,然而这一适应的分子机制仍不清楚.本研究选择在细胞感知和适应内环境氧分压变化的过程中发挥重要作用的低氧诱导因子(Hy-poxia-induci...     

Parallel evolution of IDH2 gene in cetaceans,primates and bats

Cetaceans and primates both have large brains that require large amounts of aerobic energy metabolism. In bats, the cost of flight makes locomotion energetically demanding. These mammalian groups may represent three independent evolutionary origins of an energy-demanding lifestyle in mammals. IDH2 encodes an enzyme in the tricarboxylic acid cycle in the mitochondrion, which plays a key role in aerobic energy metabolism. In this study, we cloned and sequenced this gene in two cetaceans, and 19 bat species, and compared the data with available primate sequences to test its evolution. We found significant signals of parallel evolution in this gene among these three groups. Parallel evolution of this gene may reflect their parallel evolution towards a higher demand for energy.     

Heterothermy,body size,and locomotion as ecological predictors of migration in mammals

1. Migration is ubiquitous among animals and has evolved repeatedly and independently. Comparative studies of the evolutionary origins of migration in birds are widespread, but are lacking in mammals. Mammalian species have greater variation in functional traits that may be relevant for migration. Interspecific variation in migration behaviour is often attributed to mode of locomotion (i.e. running, swimming, and flying) and body size, but traits associated with the evolutionary precursor hypothesis, including geographic distribution, habitat, and diet, could also be important predictors of migration in mammals. Furthermore, mammals vary in thermoregulatory strategies and include many heterothermic species, providing an alternative strategy to avoid seasonal resource depletion.
2. We tested the evolutionary precursor hypothesis for the evolution of migration in mammals and tested predictions linking migration to locomotion, body size, geographic distribution, habitat, diet, and thermoregulation. We compiled a dataset of 722 species from 27 mammalian orders and conducted a series of analyses using phylogenetically informed models.
3. Swimming and flying mammals were more likely to migrate than running mammals, and larger species were more likely to migrate than smaller ones. However, heterothermy was common among small running mammals that were unlikely to migrate. High-latitude swimming and flying mammals were more likely to migrate than high-latitude running mammals (where heterothermy was common), and most migratory running mammals were herbivorous. Running mammals and frugivorous bats with high thermoregulatory scope (greater capacity for heterothermy) were less likely to migrate, while insectivorous bats with high thermoregulatory scope were more likely to migrate.
4. Our results indicate a broad range of factors that influence migration, depending on locomotion, body size, and thermoregulation. Our analysis of migration in mammals provided insight into some of the general rules of migration, and we highlight opportunities for future investigations of exceptions to these rules, ultimately leading to a comprehensive understanding of the evolution of migration.

     

Micro-anatomy of the volar skin and interordinal relationships of primates

Paleontological and molecular evidence have been employed to suggest that flying lemurs (Dermoptera) and primates form a monophyletic group, in sharp contrast with cranial and postcranial evidence indicating sister group relationships between flying lemurs and bats (Chiroptera). New evidence from the epidermis of the volar pads of primates, tree shrews, flying lemurs, bats, and other mammals was examined and mapped on to various hypotheses of archontan relationships. The micro-anatomy of the skin on the palm and sole of flying lemurs and bats differs fundamentally from that of tree shrews (Scandentia) and primates. The volar skin of flying lemurs and bats lacks the serial arrangement of papillary ridges and grooves ("fingerprints") found in primates, tree shrews, and many other mammals. Moreover, the junction between the epidermis and dermis in flying lemurs and bats is relatively flat and shows little or no development of the internal ridges that occur in primates and tree shrews. When mapped on to a set of cladograms of mammals currently allocated to the superorder Archonta, this new evidence does not support sister group relationships between flying lemurs and primates, regardless of the volar skin morphology that characterized the last common ancestor of Archonta. Micro-anatomical differences that distinguish the volar skin of flying lemurs and bats from that of primates and tree shrews reflect a profound dichotomy in the functional roles fulfilled by the extremities, which could be significant in a phylogenetic context.     

Comparative genomics analyses of alpha-keratins reveal insights into evolutionary adaptation of marine mammals

Background

Diversity of hair in marine mammals was suggested as an evolutionary innovation to adapt aquatic environment, yet its genetic basis remained poorly explored. We scanned α-keratin genes, one major structural components of hair, in 16 genomes of mammalian species, including seven cetaceans, two pinnipeds, polar bear, manatee and five terrestrial species.

Results

Extensive gene loss and high pseudogenization rate of α-keratin genes were identified in cetaceans when compared to terrestrial artiodactylans (average number of α-keratins 37.29 vs. 58.33; pseudogenization rate 29.89% vs. 8.00%), especially of hair follicle-specific keratin genes (average pseudogenization rate in cetaceans of 43.88% relative to 3.80% artiodactylian average). Compared to toothed whale, the much more number of intact functional α-keratin genes was examined in the baleen whale that had specific keratinized baleen. In contrast, the number of keratin genes in pinnipeds, polar bear and manatee were comparable to those of their respective terrestrial relatives. Additionally, four keratin genes (K39, K9, K42, and K74) were found to be pseudogenes or lost uniquely in cetaceans and manatees.

Conclusions

Species-specific evolution of α-keratin gene family identified in the marine mammals might be responsible for their different hair characteristics. Increased gene loss and pseudogenization rate identified in cetacean lineages was likely to contribute to hair-less phenotype to adaptation for complete aquatic environment. However, the fully aquatic manatee still remained the comparable number of intact genes to its terrestrial relative, probably due to its perioral bristles and bristle-like hairs on the oral disk. By contrast, similar evolution pattern of α-keratin gene repertoire in the pinnipeds, polar bear and their terrestrial relatives was likely due to abundant hair to keep warm when they went ashore. Interestingly, some keratin genes were exclusively lost in cetaceans and manatees, likely as a result of convergent hair-loss phenotype to inhabit completely aquatic environment in both groups.

     

Energetic and biomechanical constraints on animal migration distance

Animal migration is one of the great wonders of nature, but the factors that determine how far migrants travel remain poorly understood. We present a new quantitative model of animal migration and use it to describe the maximum migration distance of walking, swimming and flying migrants. The model combines biomechanics and metabolic scaling to show how maximum migration distance is constrained by body size for each mode of travel. The model also indicates that the number of body lengths travelled by walking and swimming migrants should be approximately invariant of body size. Data from over 200 species of migratory birds, mammals, fish, and invertebrates support the central conclusion of the model - that body size drives variation in maximum migration distance among species through its effects on metabolism and the cost of locomotion. The model provides a new tool to enhance general understanding of the ecology and evolution of migration.     

Interactions between locomotion and ventilation in tetrapods

Interactions between locomotion and ventilation have now been studied in several species of reptiles, birds and mammals, from a variety of perspectives. Among these perspectives are neural interactions of separate but linked central controllers; mechanical impacts of locomotion upon ventilatory pressures and flows; and the extent to which the latter may affect gas exchange and the energetics of exercise. A synchrony, i.e. 1:1 pattern of coordination, is observed in many running mammals once they achieve galloping speeds, as well as in flying bats, some flying birds and hopping marsupials. Other, non-1:1, patterns of coordination are seen in trotting and walking quadrupeds, as well as running bipedal humans and running and flying birds. There is evidence for an energetic advantage to coordination of locomotor and respiratory cycles for flying birds and running mammals. There is evidence for a mechanical constraint upon ventilation by locomotion for some reptiles (e.g. iguana), but not for others (e.g. varanids and crocodilians). In diving birds the impact of wing flapping or foot paddling on differential air sac pressures enhances gas exchange during the breath hold by improving diffusive and convective movement of air sac oxygen to parabronchi. This paper will review the current state of our knowledge of such influences of locomotion upon respiratory system function.     

The relationship between body mass and relative investment in testes mass in amniotes and other vertebrates

In terrestrial placental mammals, there is a well‐known negative allometric relationship between body mass and relative investment in testes mass. Such a negative relationship means that males of relatively monogamous small species invest proportionately more in their reproductive tissues than males of more polyandrous larger species. The selective pressure responsible for this relationship remains unclear and is it not known if this is a general allometric relationship that is similar across all vertebrate lineages. To investigate this, we conducted the first comparison of relationships between body mass and testes mass (using percentage testes mass as the dependent variable) across a variety of vertebrate groups. In all amniote lineages examined, the allometric relationship between body mass and testes mass was relatively strong and negative. We show, for the first time, that reptiles, birds and terrestrial placental mammals followed the same allometric relationship and, contrary to previous expectations, this relationship is sigmoidal rather than linear. Within this data set, there was no significant difference between this general amniote relationship and any of the 13 orders of reptiles, birds and terrestrial placental mammals examined. As a result, we propose that a sigmoidal relationship should be considered the default assumption for the form of the body mass – testes mass relationship within the amniote lineage. However, we also identify significant differences within some additional mammal groups (marsupials, bats and cetaceans). In each of these cases, only some sub‐groupings differed significantly from the general amniote relationship. In contrast to the amniotes, the relationship is relatively weak and positive in teleost fish and frogs suggesting that a negative allometric relationship is not universal in vertebrates. We explore whether variation in the body mass – testes mass relationships can be linked to sperm competition or a variety of ecological characteristics, either for amniotes in particular or vertebrates in general.     

Complete Mitochondrial Genome of a Neotropical Fruit Bat, Artibeus jamaicensis, and a New Hypothesis of the Relationships of Bats to Other Eutherian Mammals

The complete mitochondrial genome was obtained from a microchiropteran bat, Artibeus jamaicensis. The presumptive amino acid sequence for the protein-coding genes was compared with predicted amino acid sequences from several representatives of other mammalian orders. Data were analyzed using maximum parsimony, maximum likelihood, and neighbor joining. All analyses placed bats as the sister group of carnivores, perissodactyls, artiodactyls, and cetaceans (e.g., 100% bootstrap value with both maximum parsimony and neighbor joining). The data strongly support a new hypothesis about the origin of bats, specifically a bat/ferungulate grouping. None of the analyses supported the superorder Archonta (bats, flying lemurs, primates, and tree shrews). Our hypothesis regarding the relationship of bats to other eutherian mammals is concordant with previous molecular studies and contrasts with hypotheses based solely on morphological criteria and an incomplete fossil record. The A. jamaicensis mitochondrial DNA control region has a complex pattern of tandem repeats that differs from previously reported chiropteran control regions. Received: 22 January 1998 / Accepted: 3 June 1998     

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.     

Neither season nor sex affects the cost of terrestrial locomotion in a circumpolar diving duck: the common eider (Somateria mollissima)

Locomotion accounts for a significant proportion of the energy budget in birds, and selection is likely to act on its economy, particularly where energy conservation is essential for survival. Birds are capable of different forms of locomotion, such as walking/running, swimming, diving and flying, and adaptations for these affect the energetic cost [cost of locomotion (CoL)] and kinematics of terrestrial locomotion. Furthermore, seasonal changes in climate and photoperiod elicit physiological and behavioural adaptations for survival and reproduction, which also influence energy budget. However, little is understood about how this might affect the CoL. Birds are also known to exhibit sex differences in size, behaviour and physiology; however, sex differences in terrestrial locomotion have only been studied in two cursorially adapted galliform species in which males achieved higher maximum speeds, and in one case had a lower mass-specific CoL than females. Here, using respirometry and high-speed video recordings, we sought to determine whether season and sex would affect the CoL and kinematics of a principally aquatic diving bird: the circumpolar common eider (Somateria mollissima). We demonstrate that eiders are only capable of a walking gait and exhibit no seasonal or sex differences in mass-specific CoL or maximum speed. Despite sharing identical limb morphometrics, the birds exhibited subtle sex differences in kinematic parameters linked to the greater body mass of the males. We suggest that their principally aquatic lifestyle accounts for the observed patterns in their locomotor performance. Furthermore, sex differences in the CoL may only be found in birds in which terrestrial locomotion directly influences male reproductive success.     

Comparative trends in shortening velocity and force production in skeletal muscles

Skeletal muscles are diverse in their properties, with specific contractile characteristics being matched to particular functions. In this study, published values of contractile properties for >130 diverse skeletal muscles were analyzed to detect common elements that account for variability in shortening velocity and force production. Body mass was found to be a significant predictor of shortening velocity in terrestrial and flying animals, with smaller animals possessing faster muscles. Although previous studies of terrestrial mammals revealed similar trends, the current study indicates that this pattern is more universal than previously appreciated. In contrast, shortening velocity in muscles used for swimming and nonlocomotory functions is not significantly affected by body size. Although force production is more uniform than shortening velocity, a significant correlation with shortening velocity was detected in muscles used for locomotion, with faster muscles tending to produce more force. Overall, the contractile properties of skeletal muscles are conserved among phylogenic groups, but have been significantly influenced by other factors such as body size and mode of locomotion.     

Increased rate of hair keratin gene loss in the cetacean lineage

Background

Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially explain the phenotypic hair features of different lineages, we characterized the type I and II clusters of alpha keratins from eight mammalian species, including the hairless dolphin and minke whale representing the order Cetacea.

Results

We combined the available genomic information with phylogenetic analysis to conduct a comprehensive analysis of the evolutionary patterns of keratin gene clusters. We found that both type I and II gene clusters are fairly conserved among the terrestrial mammals included in this study, with lineage specific gene duplication and gene loss. Nevertheless, there is also evidence for an increased rate of pseudogenization in the cetacean lineage when compared to their terrestrial relatives, especially among the hair type keratins.

Conclusions

Here we present a comprehensive characterization of alpha-keratin genes among mammals and elucidate the mechanisms involved in the evolution of this gene family. We identified lineage-specific gene duplications and gene loss among the Laurasiatherian and Euarchontoglires species included in the study. Interestingly, cetaceans present an increased loss of hair-type keratin genes when compared to other terrestrial mammals. As suggested by the ‘less-is-more’ hypothesis, we do not rule out the possibility that the gene loss of hair-type keratin genes in these species might be associated to the hairless phenotype and could have been adaptive in response to new selective pressures imposed by the colonization of a new habitat. Our study provides support for the idea that pseudogenes are not simply ‘genomic fossils’ but instead have adaptive roles during the evolutionary process.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-869) contains supplementary material, which is available to authorized users.     

Molecular Cloning and Evolutionary Analysis of Hemoglobin α-Chain Genes in Bats

Bats are the only mammals with the capacity for powered flight. When flying, they need abundant energy and oxygen. According to previous works, the hemoglobin (Hb) oxygen loading function of bats is insensitive to variations in body temperature, although different bat species have different heat sensitivity. We cloned Hb α-chain sequences from eight bat species to investigate whether they have different characteristics. We found that Hb in the bat lineages is under purifying selection, which accords with the importance of its function in bats. Three turn regions in bat Hb, however, have distinct evolutionary rates compared with those of other mammals, and the codons in these regions have an accelerated rate of evolution. These codons are under divergent selection in bats. These changes in Hb may have occurred in response to the physiological requirements of the species concerned, as adaptations to different lifestyles.     

Independent reversals to terrestriality in squirrels (Rodentia: Sciuridae) support ecologically mediated modes of adaptation

The family Sciuridae is one of the most widespread and ecologically diverse lineages of rodents and represents an ideal model for investigating the evolution of locomotion modes and the historical biogeography of terrestrial mammals. We used a comprehensive database on locomotion modes, an updated phylogeny and novel biogeographic comparative methods to reassess the evolution of locomotion of squirrels and to investigate whether these locomotion modes evolved convergently in different continents. We found that locomotion changes occurred in different independent lineages of the family, including four reversals to terrestriality and one evolution of gliding. We also found evidence for Eurasia as the centre of origin of Sciuridae, challenging the classification of the oldest squirrel fossil records from the early Oligocene in North America. Additionally, Eurasia is also the possible centre of origin for most of squirrel subfamilies and tribes, and where locomotion changes have occurred. Parallel locomotion shifts could be explained by the adaptation towards different ecological niches followed by colonization of new continents.     

BUFFERING CAPACITY OF THE LOCOMOTOR MUSCLE IN CETACEANS: CORRELATES WITH POSTPARTUM DEVELOPMENT, DIVE DURATION, AND SWIM PERFORMANCE

Skeletal muscles of marine mammals must support the metabolic demands of exercise during periods of reduced blood flow associated with the dive response. Enhanced muscle buffering could support anaerobic metabolic processes during apnea, yet this has not been fully investigated in cetaceans. To assess the importance of this adaptation in the diving and swimming performance of cetaceans, muscle buffering capacity due to non-bicarbonate buffers was measured in the longissimus dorsi of ten species of odontocete and one mysticete. Immature specimens from a subset of these species were studied to assess developmental trends. Fetal and neonatal cetaceans have low buffering capacities (range: 34.8–53.9 slykes) that are within the range measured for terrestrial mammals. A lengthy developmental period, independent of muscle myoglobin postnatal development, is required before adult levels are attained. Adult cetacean buffering capacities (range: 63.7–94.5 slykes) are among the highest values recorded for mammals. Cetacean species that demonstrate extremely long dive durations or high burst speed swimming tend to have greater buffering capacities. However, the wide range of body size across cetaceans may complicate these trends. Enhanced muscle buffering capacity may enable small-bodied species to extend breath-hold beyond short aerobic dive limits for foraging or predator evasion when necessary.     

The macroevolutionary relationship between diet and body mass across mammals

Body mass and diet are two fundamental ecological parameters that influence many other aspects of an animal's biology. Thus, the potential physiological and ecological processes linking size and diet have been the subject of extensive research, although the broad macroevolutionary relationship between the two traits remains largely unexplored phylogenetically. Using generalized Ornstein–Uhlenbeck models and data on over 1350 species of mammal, we reveal that evolutionary changes in body mass are consistently associated with dietary changes across mammals. Best‐fitting models find that herbivores are substantially heavier than other dietary groups and that omnivores are frequently intermediate in mass between herbivores and carnivores. Interestingly, although flying and swimming both place very different physical constraints on mass, bats still follow the general mammalian pattern but marine mammals do not. Such differences may be explained by reduced gravitational constraints on size in water along with ecological differences in food availability between aquatic and terrestrial realms, allowing marine carnivores to become the largest mammals on earth. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 173–184.